Contacts of the strand formed by residues 57 - 67 (chain M) 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 M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M ASN* 3.6 8.1 - - - -
54M THR* 2.8 43.5 + - - +
55M GLN 4.2 8.5 - - - -
56M GLY* 1.3 80.5 - - - +
58M ASP* 1.3 63.4 + - - +
60M GLU* 3.8 7.0 + - - +
77M ARG* 3.6 27.1 - - - +
123M TYR* 2.9 38.1 + - - -
124M PHE 4.6 1.0 + - - -
126M GLU* 3.5 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M ASN* 3.0 14.1 + - - +
56M GLY 4.2 1.4 + - - -
57M ARG* 1.3 72.0 - - - +
59M ASN* 1.3 78.6 + - - +
60M GLU 3.3 0.4 - - - -
77M ARG* 2.9 33.7 + - + +
137M GLN 2.8 11.1 - - - +
138M ASP* 3.4 21.0 - - - +
325M CA 2.4 31.4 - - - -
348M CPJ 3.3 6.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M TYR 4.7 0.2 - - - -
53M ASN* 3.0 12.5 + - - -
58M ASP* 1.3 79.4 + - - +
60M GLU* 1.3 62.1 + - - +
61M LEU* 3.4 3.3 + - - +
62M LEU* 3.7 10.3 - - + +
74M TYR* 3.9 24.6 - - + +
76M GLY 3.5 1.6 + - - -
77M ARG* 2.8 32.5 + - + +
136M GLU* 3.1 9.1 - - - +
325M CA 2.4 26.2 - - - -
348M CPJ 3.2 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M TYR* 3.4 23.3 + - + +
54M THR* 3.9 23.6 - - + +
57M ARG* 3.8 17.1 - - - +
58M ASP 3.2 1.2 + - - -
59M ASN* 1.3 76.8 - - - +
61M LEU* 1.3 62.0 + - - +
75M ILE* 3.4 5.0 - - - -
76M GLY* 2.8 22.7 + - - +
77M ARG* 3.2 19.1 + - - -
123M TYR* 2.6 29.8 + - - -
125M VAL* 3.3 13.6 - - + +
126M GLU* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M PHE* 3.6 46.2 - - + -
35M LEU* 5.3 1.8 - - + -
50M PHE* 3.9 14.5 - - + +
52M TYR* 2.9 69.3 + - + +
59M ASN 3.4 0.2 - - - -
60M GLU* 1.3 79.4 - - - +
62M LEU* 1.3 66.1 + - - +
63M VAL* 4.9 3.6 - - + -
73M LEU* 3.9 13.7 - - + -
74M TYR 3.2 5.6 - - - +
75M ILE* 4.5 2.5 - - + -
125M VAL* 4.4 10.8 - - + -
159M MET* 3.8 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M SER* 3.3 27.8 - - - +
50M PHE 3.3 11.0 - - - +
51M SER* 3.8 9.4 - - - +
52M TYR 5.1 0.2 - - - +
53M ASN* 6.0 0.2 - - - +
59M ASN* 3.7 16.4 - - - +
61M LEU* 1.3 77.9 - - - +
63M VAL* 1.3 62.9 - - - +
64M TYR* 3.9 10.3 + - + -
72M SER 3.5 1.6 - - - +
73M LEU* 3.3 6.3 - - - +
74M TYR* 2.8 55.7 + - + -
136M GLU* 3.4 22.9 - - + +
348M CPJ 3.3 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35M LEU* 3.7 30.5 - - + -
37M PHE* 4.3 10.5 - - + -
48M SER* 3.8 2.9 + - - -
49M LEU* 2.8 46.4 + - + -
50M PHE* 2.9 22.4 + - + +
61M LEU* 4.9 1.8 - - + -
62M LEU* 1.3 73.7 - - - +
64M TYR* 1.3 61.9 + - - +
71M TYR* 5.3 2.7 - - + -
72M SER 3.4 7.6 - - - +
73M LEU* 4.5 7.2 - - + -
94M ILE* 4.9 3.1 - - + -
96M VAL* 3.8 16.2 - - + -
107M PHE* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M ALA* 3.3 33.2 - - + +
47M TYR 3.6 21.5 - - - -
48M SER* 3.9 12.3 - - - -
49M LEU* 5.3 0.7 - - - -
62M LEU* 4.2 14.4 - - + -
63M VAL* 1.3 76.9 - - - +
65M LYS* 1.3 58.1 + - - +
66M GLU* 3.6 31.6 + - - -
71M TYR* 4.0 1.4 - - - -
72M SER* 2.8 40.1 + - - +
74M TYR* 4.1 22.9 - + + -
136M GLU* 4.4 3.6 - - + -
148M GLN* 3.1 37.3 + - + +
348M CPJ 3.5 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M LEU 5.7 1.6 + - - -
45M ARG 4.4 1.1 - - - +
46M ALA* 3.2 2.6 - - - -
47M TYR* 2.9 78.7 + - + +
49M LEU* 4.2 8.4 - - + +
63M VAL 4.3 0.2 - - - -
64M TYR* 1.3 71.4 - - - +
66M GLU* 1.3 62.3 - - - +
67M ARG* 3.4 23.3 - - - +
68M VAL* 4.2 10.3 - - - +
69M GLY 4.0 2.5 - - - +
70M GLU 3.8 5.4 - - - +
71M TYR* 3.4 36.7 + - + +
86M GLU* 3.1 27.7 + - - -
88M PHE* 5.7 3.6 - - - -
92M VAL* 6.1 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M SER 4.8 0.2 - - - +
45M ARG 4.4 0.3 - - - -
46M ALA* 3.5 27.8 + - - +
64M TYR* 3.7 15.8 - - - +
65M LYS* 1.3 71.6 - - - +
67M ARG* 1.3 77.5 + - + +
70M GLU* 3.5 27.0 + - - +
72M SER* 2.7 35.8 + - - +
74M TYR* 3.9 6.1 + - - -
79M LYS* 2.8 28.1 + - - -
81M THR* 4.8 4.0 - - + -
348M CPJ 5.7 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M SER 4.4 12.8 - - - +
45M ARG 5.3 1.1 - - - -
65M LYS* 3.4 12.9 - - - -
66M GLU* 1.3 91.8 + - - +
68M VAL* 1.3 73.6 + - - +
69M GLY 3.2 0.5 + - - -
70M GLU* 2.8 62.0 + - - +
----------------------------------------------------------
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