Contacts of the strand formed by residues 34 - 45 (chain C) in PDB entry 2WJ7
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 VAL 34 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LYS 3.7 0.3 - - - +
30C VAL* 3.6 2.9 - - - +
31C LEU* 3.1 37.2 + - + +
32C GLY 3.3 2.6 - - - -
33C ASP* 1.3 89.3 - - + +
35C ILE* 1.3 67.4 + - - +
36C GLU* 3.7 7.1 + - + +
58C LYS* 3.8 31.2 - - + -
59C TYR 3.2 16.4 - - - +
60C ARG* 5.3 4.7 - - + -
61C ILE* 3.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 4.3 21.1 - - + -
14C VAL* 6.3 2.2 - - + -
28C VAL* 4.3 15.5 - - + -
29C LYS 3.7 4.0 - - - -
30C VAL* 4.5 11.4 - - + +
34C VAL* 1.3 73.0 - - - +
36C GLU* 1.3 67.8 + - - +
37C VAL* 4.2 10.1 - - + -
57C ARG 3.6 0.9 - - - +
58C LYS* 3.2 4.0 - - - -
59C TYR* 2.9 62.0 + - + +
60C ARG 5.4 0.4 - - - +
61C ILE* 3.8 28.9 - - + +
62C PRO* 6.1 0.2 - - + -
70C ILE* 5.3 3.1 - - + -
82C VAL* 4.0 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LYS 3.5 1.6 - - - +
28C VAL* 3.3 6.1 - - - +
29C LYS* 3.0 46.2 + - + +
31C LEU* 3.8 21.7 - - + +
34C VAL* 4.4 10.7 - - + +
35C ILE* 1.3 74.4 - - - +
37C VAL* 1.3 61.8 + - - +
38C HIS 4.1 0.7 - - - +
56C HIS* 3.4 30.4 + - + -
57C ARG 3.2 4.9 - - - -
58C LYS* 4.3 12.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU* 4.4 11.4 - - + -
26C LEU* 4.9 3.8 - - + -
27C LYS 3.5 7.2 - - - +
28C VAL* 4.4 11.7 - - + -
35C ILE* 4.2 15.7 - - + -
36C GLU* 1.3 77.6 - - - +
38C HIS* 1.3 66.1 + - - +
55C PHE* 3.6 25.7 - - + -
56C HIS* 3.3 4.2 + - - -
57C ARG* 2.8 44.6 + - + -
59C TYR* 4.3 17.3 - - + -
80C LEU* 4.1 22.4 - - + -
82C VAL* 4.8 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU 3.8 1.9 - - - +
26C LEU* 3.4 6.4 - - - +
27C LYS* 2.9 55.8 + - + +
36C GLU* 4.1 0.8 - - + -
37C VAL* 1.3 78.1 - - - +
39C GLY* 1.3 63.1 + - - +
40C LYS* 3.7 19.3 - - + +
54C GLU* 2.7 42.3 + - + -
55C PHE 3.3 9.4 + - - -
56C HIS* 3.9 25.8 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 3.7 8.1 - - - -
25C GLU 3.4 8.1 - - - -
26C LEU* 4.0 6.1 - - - -
38C HIS* 1.3 76.2 - - - +
40C LYS* 1.3 60.9 + - - -
54C GLU* 3.3 5.5 - - - +
55C PHE* 2.9 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 3.5 4.9 - - - -
25C GLU* 3.2 32.3 + - - +
38C HIS* 3.7 15.0 - - + +
39C GLY* 1.3 74.6 - - - +
41C HIS* 1.3 67.8 + - - +
42C GLU* 3.5 25.1 + - + +
53C ARG 3.3 7.9 - - - +
54C GLU* 2.8 37.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C HIS 3.5 13.0 + - - -
21C PHE* 4.0 14.1 - - + -
25C GLU* 3.6 26.7 - - - +
40C LYS* 1.3 81.6 + - - +
42C GLU* 1.3 86.6 + - - +
44C ARG* 3.6 26.4 + - - +
51C ILE* 3.1 19.0 + - - +
52C SER* 3.2 8.4 - - - -
53C ARG* 2.7 68.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLU* 5.0 1.4 + - - -
40C LYS* 3.5 29.1 + - + +
41C HIS* 1.3 94.9 - - - +
43C GLU* 1.3 69.5 + - - +
44C ARG* 3.8 3.3 + - - +
52C SER* 3.7 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 1.3 77.9 + - - +
44C ARG* 1.3 64.9 + - - +
50C PHE* 3.8 29.6 - - + -
51C ILE* 3.6 14.4 - - - +
52C SER* 3.6 11.9 - - - +
56D HIS 5.6 0.7 - - - +
58D LYS* 5.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C HIS* 3.0 25.0 + - - +
22C SER* 4.9 3.4 + - - +
25C GLU* 3.2 37.4 + - - -
41C HIS* 3.6 29.4 - - - -
42C GLU 3.8 4.9 + - - +
43C GLU* 1.3 81.4 - - - +
45C GLN* 1.3 78.9 + - + +
46C ASP* 3.5 3.0 + - - -
50C PHE* 3.5 5.8 - - - -
51C ILE* 3.1 31.2 + - - +
53C ARG* 4.6 2.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ARG* 1.3 91.4 - - - +
46C ASP* 1.3 63.7 - - - +
49C GLY 3.1 13.2 - - - +
50C PHE* 3.1 35.8 - - + -
----------------------------------------------------------
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