Contacts of the strand formed by residues 34 - 42 (chain B) in PDB entry 5EWL
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 SER 34 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B PRO 3.9 0.9 + - - -
33B PRO* 1.3 78.1 - - - +
35B ILE* 1.4 66.3 + - - +
36B GLY 4.5 0.2 + - - -
64B VAL* 4.6 0.5 - - - +
65B VAL* 3.2 19.1 - - - -
67B ARG* 4.6 15.3 - - - -
92B ARG* 4.9 8.9 + - - -
314B ILE* 5.5 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B SER* 1.4 75.0 - - - +
36B GLY* 1.3 58.5 + - - +
37B ILE* 3.6 18.6 + - + +
64B VAL* 3.6 27.8 - - + -
65B VAL 2.8 19.8 + - - +
66B PRO* 3.5 6.0 - - + +
67B ARG* 2.7 33.1 + - - -
92B ARG* 4.4 1.6 - - - -
95B GLN* 3.7 24.7 - - + +
300B ILE* 4.1 8.5 - - + -
301B THR* 3.7 30.3 - - - +
304B ALA* 3.9 14.4 - - + -
314B ILE* 3.8 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 1.3 71.4 - - - +
37B ILE* 1.4 59.4 + - - -
67B ARG 3.7 3.4 - - - -
92B ARG* 3.5 37.2 - - - +
93B LYS 4.0 5.7 + - - -
94B ILE* 3.4 7.4 - - - -
95B GLN* 2.7 36.1 + - - +
96B GLY 3.7 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ILE* 3.6 11.6 + - + +
36B GLY* 1.4 76.2 - - - +
38B ALA* 1.3 65.0 + - - +
39B VAL* 4.0 2.4 + - + -
66B PRO* 3.8 15.0 - - + -
67B ARG 3.3 7.0 + - - +
68B VAL* 3.3 11.7 - - + +
69B GLU* 3.0 25.7 + - - +
94B ILE* 4.0 2.7 - - - -
96B GLY 3.5 12.1 - - - +
98B VAL* 4.2 15.5 - - + -
297B ILE* 3.8 22.9 - - + +
300B ILE* 3.8 39.0 - - + -
301B THR* 3.4 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 1.3 72.2 - - - +
39B VAL* 1.3 60.1 + - - +
40B ILE* 3.8 1.3 - - + -
69B GLU* 3.7 10.5 - - - +
71B VAL* 5.0 1.1 - - + -
88B LEU* 3.8 28.7 - - + -
94B ILE* 3.8 27.1 - - + +
96B GLY 3.3 7.1 + - - -
97B VAL* 3.4 11.8 - - + +
98B VAL* 2.9 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 4.6 2.7 - - + -
38B ALA* 1.3 71.1 - - - +
40B ILE* 1.3 57.7 - - - +
41B LEU* 3.7 24.8 + - + +
68B VAL* 3.7 26.0 - - + -
69B GLU 3.0 9.7 + - - -
70B LEU* 3.6 16.9 - - + -
71B VAL 2.8 30.7 + - - +
98B VAL* 3.3 23.3 - - + +
126B ILE* 6.0 0.2 - - + -
293B VAL* 3.6 35.4 - - + -
297B ILE* 4.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ALA* 3.8 2.2 - - + -
39B VAL* 1.3 71.8 - - - +
41B LEU* 1.3 64.4 + - - +
42B VAL* 4.6 0.9 - - + -
71B VAL* 3.4 12.8 - - + +
73B MET* 3.7 29.8 - - + -
84B ARG* 5.1 2.9 - - + -
85B ILE* 3.6 32.5 - - + +
88B LEU* 3.8 28.5 - - + -
97B VAL* 3.7 19.1 - - + -
98B VAL 2.9 9.2 + - - +
99B PHE* 3.6 30.7 - - + -
100B ALA 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B VAL* 4.1 17.7 - - + +
40B ILE* 1.3 74.7 - - - +
42B VAL* 1.3 64.2 + - - +
43B GLY 3.6 6.5 + - - +
45B SER* 3.8 24.0 + - - +
47B GLU* 5.4 2.7 - - + -
50B ILE* 4.0 12.3 - - + -
70B LEU* 3.9 36.3 - - + -
71B VAL 2.8 13.8 + - - +
72B ALA* 3.7 8.0 - - + +
73B MET 3.3 18.2 + - - +
100B ALA* 3.5 25.4 - - + -
289B LEU* 4.1 20.0 - - + -
293B VAL* 4.5 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 42 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 1.3 70.5 - - - +
43B GLY* 1.3 63.9 + - - +
44B THR 5.3 0.3 - - - +
45B SER* 6.0 0.3 - - - -
73B MET* 3.4 35.7 - - + +
74B ASN 5.0 6.1 - - - +
76B THR* 3.4 28.9 - - + -
99B PHE* 3.7 29.2 - - + -
100B ALA 2.9 7.2 + - - +
101B ASP* 3.6 26.5 - - + -
102B ASP* 3.2 22.3 + - - +
103B THR* 4.2 4.5 - - + -
----------------------------------------------------------
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