Contacts of the helix formed by residues 62 - 72 (chain A) in PDB entry 5LSW
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 62 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ILE* 3.7 12.2 + - + +
29A LEU* 3.8 28.3 - - + +
30A SER* 4.9 4.4 + - - -
56A LEU* 3.5 40.4 - - + +
59A SER* 2.5 28.8 + - - -
60A PHE 3.2 2.6 + - - -
61A GLY* 1.3 74.5 - - - +
63A ILE* 1.3 67.5 + - - +
65A ALA* 3.0 8.4 + - - +
66A LEU* 3.0 26.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.1 13.0 + - + +
57A TRP* 3.6 68.6 - - + +
59A SER 4.7 1.2 + - - +
61A GLY 3.5 0.2 - - - -
62A THR* 1.3 75.0 - - - +
64A ALA* 1.3 64.2 + - - +
66A LEU* 3.1 22.3 + - + +
67A LEU* 3.0 40.6 + - + +
97A LEU* 4.7 9.0 - - + -
100A VAL* 4.6 7.6 - - + -
115A ILE* 4.7 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY* 3.4 16.7 + - - +
62A THR 3.3 0.4 - - - -
63A ILE* 1.3 79.0 - - - +
65A ALA* 1.3 58.8 + - - +
67A LEU* 3.9 11.1 - - - +
68A GLN* 3.1 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.6 29.2 - - + +
30A SER* 4.9 3.6 - - - -
35A ARG* 4.0 14.2 + - - +
61A GLY 2.9 17.8 + - - +
62A THR* 3.0 8.5 + - - +
64A ALA* 1.3 76.3 - - - +
66A LEU* 1.3 64.8 + - + +
68A GLN* 3.4 11.0 + - - +
69A GLU* 3.2 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.5 9.2 - - + -
35A ARG* 6.1 0.9 - - - -
39A LEU* 3.6 31.4 - - + -
56A LEU* 4.8 6.1 - - + -
62A THR* 3.0 24.8 + - + +
63A ILE* 3.6 19.3 - - + +
65A ALA* 1.3 78.8 - - - +
67A LEU* 1.3 62.5 + - - +
69A GLU* 3.4 8.8 + - + +
70A ILE* 3.3 24.9 + - - +
93A ALA* 4.0 12.2 - - + +
96A LEU* 4.1 27.6 - - + -
97A LEU* 3.8 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.0 29.5 + - + +
64A ALA* 3.9 8.7 - - - +
66A LEU* 1.3 73.3 - - - +
68A GLN* 1.3 60.7 + - - +
70A ILE* 3.3 8.7 + - + +
71A VAL* 2.9 33.7 + - + +
97A LEU* 4.2 12.8 - - + -
115A ILE* 3.6 47.3 - - + -
118A PHE* 4.0 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 4.4 20.2 + - - +
64A ALA 3.1 19.1 + - - +
65A ALA* 3.7 10.4 - - - +
66A LEU 3.3 0.6 - - - -
67A LEU* 1.3 74.2 - - - +
69A GLU* 1.3 59.0 + - - +
71A VAL* 4.2 6.2 - - + +
72A ASN* 2.9 54.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 2.9 27.3 + - - +
39A LEU* 4.0 13.5 - - + -
65A ALA 3.2 15.1 + - - +
66A LEU* 3.5 9.6 - - - +
67A LEU 3.3 0.2 - - - -
68A GLN* 1.3 78.3 - - - +
70A ILE* 1.3 63.6 - - - +
72A ASN* 3.4 22.6 + - - +
73A ILE* 3.9 9.9 + - - +
89A ARG* 2.7 60.2 + - - +
90A VAL* 4.2 9.4 + - - +
93A ALA* 4.1 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU 3.3 10.6 + - - +
67A LEU* 3.3 17.3 + - + +
69A GLU* 1.3 76.1 - - - +
71A VAL* 1.3 65.0 + - + +
73A ILE* 3.2 24.3 - - - +
74A TYR* 3.8 9.4 - - + +
90A VAL* 3.8 20.9 - - + -
93A ALA* 5.0 4.5 - - + -
94A LEU* 3.6 19.7 - - + +
97A LEU* 3.4 32.5 - - + -
118A PHE* 3.8 24.0 - - + +
119A LEU* 4.1 7.9 - - + -
122A PHE* 3.7 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 2.9 20.0 + - + +
68A GLN* 4.2 6.7 - - + +
70A ILE* 1.3 78.1 - - + +
72A ASN* 1.3 65.9 + - - +
73A ILE 3.0 1.6 + - - -
74A TYR* 3.1 41.1 + - + +
75A PRO* 3.8 4.2 - - - +
118A PHE* 3.9 32.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 5.3 3.8 - - - +
68A GLN* 2.9 46.8 + - - +
69A GLU* 3.5 21.2 + - - +
70A ILE 3.1 0.6 - - - -
71A VAL* 1.3 79.4 - - - +
73A ILE* 1.3 61.5 + - + +
74A TYR 3.5 0.2 - - - -
75A PRO* 3.8 10.7 - - - +
76A SER* 5.2 1.9 + - - -
86A GLN* 5.4 1.7 + - - -
89A ARG* 5.7 1.4 - - - +
----------------------------------------------------------
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