Contacts of the helix formed by residues 49 - 60 (chain D) in PDB entry 2Q2U
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 ASN 49 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 3.1 5.6 + - + +
48D ARG* 1.3 73.3 - - - +
50D SER* 1.3 60.1 + - - +
51D VAL* 3.2 5.8 + - - +
52D MET* 2.6 38.2 + - - +
53D ASN* 3.0 17.3 + - - +
81D ALA 3.1 21.6 + - - +
82D VAL* 3.4 12.6 + - - +
84D THR 3.2 16.0 + - - +
86D HIS* 3.7 17.4 - - - +
89D TYR* 3.4 28.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE 4.6 0.4 + - - -
48D ARG 2.8 15.2 + - - -
49D ASN* 1.3 68.2 - - - +
51D VAL* 1.3 58.5 + - - +
53D ASN* 3.7 8.0 - - - +
54D ARG* 2.7 38.9 + - - +
85D GLY* 5.8 0.9 - - - -
86D HIS 3.9 14.1 + - - -
87D LYS* 5.8 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D ASN* 3.2 3.0 + - - +
50D SER* 1.3 77.4 - - - +
52D MET* 1.3 59.1 + - + +
54D ARG* 4.0 14.1 + - - +
55D LEU* 2.9 52.9 + - + +
86D HIS 3.8 9.0 - - - +
87D LYS 3.6 20.0 - - - +
88D MET* 3.8 7.4 - - + -
89D TYR* 3.1 58.6 - - + +
131D GLN* 4.7 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ILE* 4.8 4.7 - - + -
49D ASN* 2.6 32.6 + - - +
51D VAL* 1.3 70.8 - - - +
53D ASN* 1.3 60.6 + - - +
55D LEU* 3.0 1.6 + - - +
56D LEU* 2.7 43.6 + - + +
68D ILE* 3.8 14.6 - - + -
70D ILE* 4.2 8.7 - - + -
81D ALA* 3.2 31.0 - - + +
82D VAL* 3.7 24.0 - - + -
89D TYR* 4.4 7.9 - - + -
93D PHE* 3.6 59.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLN* 3.3 20.8 + - - +
39D MET* 3.0 55.8 + - - +
46D PRO* 4.1 1.2 - - - +
47D ILE* 3.3 29.2 + - + +
49D ASN 3.0 10.1 + - - +
50D SER* 3.7 9.2 - - - +
52D MET* 1.3 78.9 - - - +
54D ARG* 1.3 58.7 - - - +
56D LEU* 3.5 0.4 + - - -
57D THR* 2.5 37.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D SER* 2.7 25.1 + - - +
51D VAL* 4.0 12.4 + - - +
53D ASN* 1.3 72.2 - - - +
55D LEU* 1.3 87.7 + - - +
57D THR* 3.1 16.6 + - - -
58D GLU* 2.8 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D VAL* 2.9 42.7 + - + +
52D MET* 3.5 3.4 - - - +
54D ARG* 1.3 93.6 - - - +
56D LEU* 1.3 62.6 + - - +
58D GLU* 3.0 25.4 + - - +
59D LEU* 2.9 24.9 - - + +
93D PHE* 4.3 4.7 - - + -
129D HIS* 3.7 27.1 - - + +
131D GLN* 3.7 21.3 - - - +
132D VAL* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D MET* 3.6 35.0 - - + -
47D ILE* 6.1 0.2 - - + -
52D MET 2.7 25.0 + - - +
55D LEU* 1.3 73.2 - - - +
57D THR* 1.3 55.4 + - - +
59D LEU* 4.5 3.4 - - + +
60D LEU* 2.8 56.8 + - + +
68D ILE* 4.0 20.2 - - + -
93D PHE* 4.3 13.9 - - + -
95D TYR* 3.8 31.4 - - + -
132D VAL* 3.8 18.2 - - + -
134D ILE* 5.1 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LYS* 3.3 29.9 + - - +
37D THR 3.3 24.2 - - - +
38D GLN* 3.7 10.7 - - - +
39D MET* 3.9 3.6 + - - +
53D ASN* 2.5 34.5 + - - -
54D ARG* 3.3 8.5 - - - -
55D LEU 3.1 0.4 - - - -
56D LEU* 1.3 76.0 - - - +
58D GLU* 1.3 59.6 + - + +
60D LEU 3.6 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D ARG* 2.8 47.7 + - + +
55D LEU* 3.0 21.9 + - - +
57D THR* 1.3 81.2 - - + +
59D LEU* 1.3 68.2 + - + +
60D LEU 4.8 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D LEU* 2.9 34.6 + - + +
56D LEU* 4.1 4.0 - - + +
58D GLU* 1.3 88.0 - - + +
60D LEU* 1.3 65.0 + - - +
61D PRO* 3.6 6.4 - - - +
119D TYR* 4.0 8.5 + - - -
125D HIS* 5.1 7.4 - - + +
126D ILE* 3.8 43.3 - - + +
129D HIS* 3.8 36.1 - - + +
132D VAL* 5.2 6.5 - - + -
134D ILE* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D LYS* 2.6 37.9 + - + -
39D MET* 3.8 15.9 - - + -
56D LEU* 2.8 41.7 + - + +
57D THR 3.6 2.9 - - - +
58D GLU 4.7 0.3 - - - -
59D LEU* 1.3 74.9 - - - +
61D PRO* 1.3 60.7 - - + +
64D SER* 3.5 23.8 - - - +
95D TYR* 3.4 46.4 - - + +
97D TRP* 4.1 17.0 - - + -
119D TYR* 4.9 0.2 - - - -
134D ILE* 4.5 14.4 - - + -
----------------------------------------------------------
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