Contacts of the helix formed by residues 27 - 49 (chain A) in PDB entry 5LQB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 27 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 1.3 82.4 + - - +
28A LYS* 1.3 66.7 + - - +
29A LYS* 4.0 11.0 + - - +
30A THR* 3.6 21.1 + - - -
31A GLN* 3.1 21.7 + - - +
152A LEU* 4.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 4.0 0.4 + - - -
27A THR* 1.3 72.9 - - - +
29A LYS* 1.3 61.3 + - - +
31A GLN* 3.3 31.0 + - - +
32A LEU* 2.8 58.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.3 10.0 + - - +
28A LYS* 1.3 77.6 - - - +
30A THR* 1.3 54.2 + - - +
32A LEU* 3.0 10.8 + - - +
33A GLN* 2.6 63.7 + - + +
115A GLU* 4.6 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 6.1 1.1 - - - -
27A THR* 3.6 21.0 + - - -
29A LYS* 1.3 77.4 - - - +
31A GLN* 1.3 64.9 + - - +
33A GLN* 3.1 15.0 + - - +
34A LEU* 2.9 28.6 + - + +
73A LEU* 4.1 16.0 - - + +
116A LEU* 3.7 17.1 - - + +
148A ILE* 5.8 0.4 - - + -
152A LEU* 4.0 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 5.7 1.5 + - - +
27A THR 3.1 10.8 + - - +
28A LYS* 3.6 42.4 + - - +
30A THR* 1.3 78.4 - - - +
32A LEU* 1.3 62.2 + - - +
34A LEU* 3.1 5.0 + - - +
35A GLU* 2.9 55.7 + - + +
149A ILE* 5.0 7.6 - - + +
152A LEU* 4.0 21.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LYS* 2.8 53.8 + - + +
29A LYS* 3.5 7.0 - - - +
31A GLN* 1.3 77.4 - - - +
33A GLN* 1.3 63.7 + - + +
35A GLU* 3.4 20.0 + - - +
36A HIS* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LYS* 2.6 43.8 + - + +
30A THR* 3.5 12.4 + - - +
32A LEU* 1.3 73.5 - - + +
34A LEU* 1.3 56.9 + - - +
36A HIS* 3.5 3.6 + - - +
37A LEU* 3.1 23.6 + - - +
112A ILE* 3.3 29.0 + - + +
115A GLU* 3.4 39.7 + - - +
116A LEU* 3.5 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A THR* 2.9 20.0 + - + +
31A GLN* 3.4 6.5 - - - +
33A GLN* 1.3 71.8 - - - +
35A GLU* 1.3 62.3 + - - +
36A HIS 3.2 1.1 - - - -
37A LEU* 3.8 4.3 - - + +
38A LEU* 2.8 33.1 + - - +
73A LEU* 4.5 4.0 - - + -
76A LEU* 5.5 0.4 - - + -
116A LEU* 3.8 22.7 - - + -
144A PHE* 5.3 3.8 - - + -
145A SER* 4.2 31.4 - - - +
148A ILE* 3.8 26.9 - - + -
149A ILE* 3.7 20.4 - - + +
152A LEU* 3.7 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLN* 2.9 49.4 + - + +
32A LEU* 3.7 22.2 - - - +
34A LEU* 1.3 76.2 - - - +
36A HIS* 1.3 60.5 + - - +
38A LEU* 3.7 4.5 - - + +
39A LEU* 3.0 30.3 + - - +
149A ILE* 4.0 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 2.9 42.1 + - + +
33A GLN* 3.8 5.8 - - - +
34A LEU 3.2 0.4 - - - -
35A GLU* 1.3 76.9 - - - +
37A LEU* 1.3 65.5 + - - +
39A LEU* 3.4 4.1 + - - +
40A ASP* 3.0 31.7 + - - +
108A ASN* 5.7 3.1 - - - -
112A ILE* 4.0 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN 3.1 14.5 + - - +
34A LEU* 3.8 5.6 - - + +
36A HIS* 1.3 75.5 - - - +
38A LEU* 1.3 66.4 + - - +
40A ASP* 3.0 5.4 + - - +
41A LEU* 2.9 45.9 + - + +
76A LEU* 4.1 24.2 - - + -
79A LEU* 4.3 6.5 - - + -
109A ILE* 3.8 35.4 - - + +
112A ILE* 4.3 10.6 - - + +
113A VAL* 3.9 16.2 - - + -
116A LEU* 4.3 12.8 - - + -
145A SER* 3.6 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU 2.8 23.2 + - - +
35A GLU* 3.7 5.8 - - + +
36A HIS 3.3 0.2 - - - -
37A LEU* 1.3 73.9 - - - +
39A LEU* 1.3 66.2 + - - +
41A LEU* 3.3 3.9 + - - +
42A GLN* 2.9 39.3 + - - +
142A ILE* 3.6 44.9 - - + +
145A SER* 4.0 12.8 + - - -
146A GLN* 3.8 19.1 - - + +
149A ILE* 4.0 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU 3.0 17.3 + - - +
36A HIS* 3.9 4.0 - - - +
38A LEU* 1.3 77.3 - - - +
40A ASP* 1.3 72.0 + - - +
42A GLN* 3.5 13.6 + - + +
43A MET* 2.8 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A HIS* 3.0 22.9 + - - +
37A LEU* 3.0 3.3 + - - +
39A LEU* 1.3 87.8 - - - +
41A LEU* 1.3 61.8 + - - +
43A MET* 3.5 12.1 + - + +
44A ILE* 3.0 33.8 + - - +
99A HIS* 3.7 26.8 + - - -
105A LEU* 4.1 5.8 - - - +
108A ASN* 3.6 20.1 - - - +
109A ILE* 4.0 23.7 - - + +
112A ILE* 5.4 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A LEU* 2.9 45.6 + - + +
38A LEU* 3.7 2.9 - - - +
40A ASP* 1.3 74.9 - - - +
42A GLN* 1.3 65.1 + - - +
44A ILE* 3.1 9.0 + - + +
45A LEU* 3.0 24.1 + - - +
79A LEU* 4.7 12.1 - - + -
83A LEU* 6.0 0.2 - - + -
86A LEU* 5.1 7.0 - - + -
109A ILE* 4.8 14.4 - - + -
137A PHE* 5.9 0.2 - - + -
138A LEU* 4.0 23.3 - - + +
141A TRP* 3.7 42.2 - - + +
142A ILE* 3.7 15.6 - - + +
145A SER* 4.5 2.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 2.9 36.3 + - - +
39A LEU* 3.6 14.7 - - + +
41A LEU* 1.3 76.4 - - - +
43A MET* 1.3 56.2 - - - +
45A LEU* 3.4 2.2 + - + +
46A ASN* 2.9 46.7 + - - +
142A ILE* 3.7 24.8 - - + +
146A GLN* 4.1 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 2.8 28.8 + - + +
40A ASP* 3.6 20.2 - - - +
41A LEU 3.2 0.2 - - - -
42A GLN* 1.3 71.8 - - - +
44A ILE* 1.3 65.4 + - + +
46A ASN* 3.8 3.6 - - - +
47A GLY* 2.8 26.7 + - - -
97A ASN 3.7 14.8 - - - +
98A PHE* 3.8 12.2 - - + -
99A HIS* 3.3 49.8 - - + +
105A LEU* 3.5 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A ASP 3.0 21.7 + - - +
41A LEU* 3.1 8.9 + - + +
43A MET* 1.3 75.2 - - + +
45A LEU* 1.3 64.9 + - - +
47A GLY* 3.0 2.3 + - - -
48A ILE* 3.0 29.1 + - + +
86A LEU* 4.6 11.0 - - + -
90A LEU* 3.7 33.2 - - + -
98A PHE* 3.6 13.5 - - + -
105A LEU* 3.7 33.2 - - + -
106A ILE* 4.9 0.4 - - + -
109A ILE* 3.9 20.4 - - + -
138A LEU* 3.8 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU 3.0 15.7 + - - +
42A GLN* 3.7 3.8 - - + +
44A ILE* 1.3 74.5 - - - +
46A ASN* 1.3 68.0 + - - +
48A ILE* 3.0 5.5 + - + +
49A ASN* 2.8 59.4 + - + +
135A VAL* 4.1 22.4 - - + -
138A LEU* 3.8 24.9 - - + +
139A ASN* 3.2 31.6 - - - +
142A ILE* 3.6 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A GLN* 2.9 31.0 + - - +
43A MET* 4.2 3.5 - - - +
45A LEU* 1.3 91.8 - - - +
47A GLY* 1.3 62.2 + - - +
48A ILE 3.5 0.2 + - - -
49A ASN* 3.9 11.0 + - - +
50A ASN* 4.9 3.1 + - - +
97A ASN* 5.3 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A MET 2.8 19.2 + - - -
44A ILE 3.0 1.3 + - - -
46A ASN* 1.3 78.6 - - - +
48A ILE* 1.3 60.8 + - - +
50A ASN* 5.3 2.3 + - - +
53A ASN* 4.8 1.0 - - - +
95A SER* 3.7 8.0 + - - -
97A ASN* 3.3 42.0 + - - -
98A PHE* 4.3 3.1 - - - -
31L TYR* 4.3 7.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ILE* 3.0 19.6 + - + +
45A LEU* 3.5 7.9 - - + +
47A GLY* 1.3 82.0 - - - +
49A ASN* 1.3 62.3 + - + +
50A ASN* 2.9 14.4 + - - +
53A ASN* 3.1 19.7 - - - +
56A LEU* 3.9 11.6 - - + +
59A MET* 4.2 23.3 - - + -
90A LEU* 4.4 8.5 - - + -
93A ALA 4.9 4.3 - - - +
95A SER* 4.7 6.1 - - - -
98A PHE* 3.8 21.3 - - + -
134A ILE* 3.4 45.1 - - + -
135A VAL* 5.1 3.8 - - + -
138A LEU* 4.4 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 2.8 36.9 + - + +
46A ASN* 3.9 6.9 + - - +
47A GLY 3.7 1.0 - - - -
48A ILE* 1.3 71.5 - - + +
50A ASN* 1.3 57.3 + - - +
51A TYR 4.1 1.2 + - - +
56A LEU* 4.2 16.3 - - - +
135A VAL* 3.9 31.8 - - + +
139A ASN* 5.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il