Contacts of the strand formed by residues 57 - 67 (chain P) in PDB entry 2A3W
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 ARG 57 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P ASN* 3.6 7.3 - - - +
54P THR* 2.8 48.0 + - - +
55P GLN 3.0 22.0 + - - -
56P GLY* 1.3 85.6 - - - +
58P ASP* 1.3 63.5 + - - +
60P GLU* 3.7 13.2 - - - +
77P ARG* 3.7 23.9 - - - +
123P TYR* 5.0 1.5 + - - -
126P GLU* 3.0 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53P ASN* 3.0 13.4 + - - +
56P GLY 4.2 1.8 + - - -
57P ARG* 1.3 72.3 - - - +
59P ASN* 1.3 71.5 + - - +
60P GLU 3.2 0.4 - - - -
77P ARG* 2.8 40.9 + - + +
137P GLN 2.9 11.3 - - - +
138P ASP* 3.3 20.5 - - - +
331P CA 2.5 30.6 - - - -
346P CPJ 3.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P TYR 4.6 0.2 - - - -
53P ASN* 3.0 10.5 + - - +
58P ASP* 1.3 80.7 + - - +
60P GLU* 1.3 63.3 + - - +
61P LEU* 3.3 4.0 + - - +
62P LEU* 3.8 15.8 - - + +
74P TYR* 3.8 28.0 - - + +
76P GLY 3.7 0.9 + - - -
77P ARG* 3.0 27.4 + - + +
136P GLU* 3.0 8.3 - - - +
331P CA 2.2 27.9 - - - -
346P CPJ 2.8 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P TYR* 3.3 22.2 + - + +
53P ASN* 4.0 0.2 + - - -
54P THR* 3.7 24.7 - - + +
57P ARG* 3.7 11.7 - - - +
58P ASP 3.2 1.6 + - - -
59P ASN* 1.3 75.1 - - - +
61P LEU* 1.3 61.6 + - - +
75P ILE* 3.4 4.3 - - - -
76P GLY* 2.9 21.7 + - - +
77P ARG* 3.1 21.9 + - - +
123P TYR* 2.6 38.0 + - - -
125P VAL* 3.4 8.4 - - + +
126P GLU* 2.9 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P PHE* 3.5 44.4 - - + -
35P LEU* 5.0 1.1 - - + -
50P PHE* 3.9 15.8 - - + +
52P TYR* 3.0 64.4 + - + +
60P GLU* 1.3 78.6 - - - +
62P LEU* 1.3 63.8 + - - +
63P VAL* 4.8 3.4 - - + -
73P LEU* 3.9 13.2 - - + -
74P TYR 3.1 6.7 - - - +
75P ILE* 4.6 3.4 - - + -
125P VAL* 4.5 11.4 - - + -
159P MET* 3.7 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P SER* 3.3 31.9 - - - +
50P PHE 3.4 12.1 - - - +
51P SER* 4.0 7.9 - - - +
52P TYR 5.1 0.2 - - - +
53P ASN* 6.0 0.2 - - - +
59P ASN* 3.8 15.9 - - - +
61P LEU* 1.3 76.0 - - - +
63P VAL* 1.3 66.8 + - - +
64P TYR* 4.1 6.7 - - + -
72P SER 3.6 1.2 - - - +
73P LEU* 3.3 6.5 - - - -
74P TYR* 2.8 59.9 + - + -
136P GLU* 3.5 24.2 - - - +
346P CPJ 3.5 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35P LEU* 4.0 19.7 - - + -
37P PHE* 4.4 8.7 - - + -
49P LEU* 3.0 46.7 + - + -
50P PHE* 3.0 21.0 + - + +
61P LEU* 4.8 3.1 - - + -
62P LEU* 1.3 78.0 - - - +
64P TYR* 1.3 61.6 + - - +
71P TYR* 5.3 2.9 - - + -
72P SER 3.4 8.1 - - - +
73P LEU* 4.2 10.1 - - + -
94P ILE* 4.9 2.9 - - + -
96P VAL* 3.8 25.8 - - + -
107P PHE* 4.1 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ALA* 3.4 30.5 - - + +
47P TYR* 3.5 23.3 - - - -
48P SER* 3.8 12.1 - - - -
49P LEU* 5.2 0.4 - - - -
62P LEU* 3.8 8.0 + - + -
63P VAL* 1.3 76.7 - - - +
65P LYS* 1.3 60.2 + - - +
66P GLU* 3.6 35.0 + - - -
71P TYR* 3.8 1.9 - - - +
72P SER* 2.8 40.7 + - - +
74P TYR* 4.0 25.6 - + + -
136P GLU* 4.4 2.2 - - + -
148P GLN* 3.2 40.1 + - + +
346P CPJ 4.2 23.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43P LEU 5.9 0.4 + - - -
45P ARG 4.4 0.7 - - - +
46P ALA* 3.2 2.3 - - - -
47P TYR* 2.8 78.5 + - + +
49P LEU* 4.2 9.9 - - + +
63P VAL 4.4 0.2 - - - -
64P TYR* 1.3 71.5 - - - +
66P GLU* 1.3 62.0 + - - +
67P ARG* 3.4 21.5 - - - +
68P VAL* 3.9 12.3 - - - +
69P GLY 3.9 0.9 - - - +
70P GLU 3.8 5.8 - - - +
71P TYR* 3.4 38.9 + - + +
86P GLU* 2.8 29.5 + - - -
88P PHE* 6.0 1.6 - - - -
92P VAL* 6.2 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P SER 4.7 0.2 - - - +
45P ARG* 4.3 0.9 - - - -
46P ALA* 3.4 27.7 + - - +
64P TYR* 3.6 23.7 - - - +
65P LYS* 1.3 71.8 - - - +
67P ARG* 1.3 75.1 + - - +
70P GLU* 3.6 27.2 + - + +
72P SER* 2.7 35.2 + - - +
74P TYR* 3.9 1.8 + - - -
79P LYS* 3.2 24.4 + - - -
81P THR* 4.7 3.8 - - + -
346P CPJ 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P SER 4.4 11.9 - - - +
45P ARG 5.4 1.1 - - - -
65P LYS* 3.4 12.4 - - - -
66P GLU* 1.3 90.0 + - - +
68P VAL* 1.3 72.8 + - - +
69P GLY 3.3 0.3 + - - -
70P GLU* 2.8 71.7 + - + +
----------------------------------------------------------
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