Contacts of the helix formed by residues 34 - 52 (chain G) in PDB entry 2WQT
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 ASN 34 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR* 5.6 7.7 + - - +
30G ILE* 3.2 30.6 + - + +
31G GLY* 2.9 9.0 + - - +
32G ILE 3.6 0.4 - - - -
33G ASP* 1.3 73.9 - - - +
35G ALA* 1.3 64.9 + - - +
36G GLU* 3.7 9.2 + - - +
37G ALA* 3.3 29.9 + - + +
38G ALA 3.3 12.3 + - - -
152G VAL* 3.3 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G ASP 3.4 7.7 + - - +
34G ASN* 1.3 73.6 - - - +
36G GLU* 1.3 65.2 + - - +
38G ALA* 3.2 3.2 + - - +
39G TYR* 3.0 35.9 + - + -
151G PHE* 4.0 25.6 - - + -
152G VAL* 4.2 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 36 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G ASN* 3.3 7.7 - - - +
35G ALA* 1.3 78.9 - - - +
37G ALA* 1.3 57.6 + - - +
39G TYR* 3.5 6.8 + - - +
40G ALA* 3.0 28.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G THR* 5.6 2.5 - - - +
6G LEU* 4.2 24.2 - - + +
30G ILE* 4.4 10.1 - - + -
34G ASN* 3.3 33.5 + - + +
35G ALA 3.2 0.4 - - - -
36G GLU* 1.3 76.4 - - - +
38G ALA* 1.3 61.1 + - - +
40G ALA* 3.1 9.8 + - - +
41G ILE* 2.9 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 38 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ILE* 4.5 6.3 - - + +
34G ASN 3.3 2.6 + - - -
35G ALA* 3.2 9.8 + - - +
37G ALA* 1.3 78.2 - - - +
39G TYR* 1.3 60.5 + - - +
41G ILE* 3.3 3.5 + - - +
42G GLN* 3.1 18.5 + - - +
152G VAL* 3.4 42.6 - - + +
155G VAL* 3.7 17.7 - - + -
156G ALA* 3.4 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 39 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G ALA* 3.0 31.3 + - + +
36G GLU* 3.9 5.4 - - - +
38G ALA* 1.3 76.7 - - - +
40G ALA* 1.3 58.3 + - - +
42G GLN* 3.5 11.1 + - - +
43G HIS* 2.9 29.0 + - - +
77G PRO 4.3 4.2 + - - -
78G ASP* 3.8 10.9 + - - -
79G PHE* 3.3 72.7 + + - -
151G PHE* 4.5 15.4 - + - -
155G VAL* 3.4 23.2 - - + +
210G TRP* 4.4 4.0 - - - -
214G LYS* 4.3 18.2 + - - -
218G LEU* 6.2 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU* 4.0 20.4 - - + -
36G GLU* 3.0 17.1 + - + +
37G ALA* 3.1 10.1 + - - +
39G TYR* 1.3 73.9 - - - +
41G ILE* 1.3 59.9 + - - +
43G HIS* 3.2 8.4 + - - +
44G ILE* 2.8 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU* 3.9 23.6 - - + +
9G LEU* 4.0 30.7 - - + -
10G ALA* 3.8 23.3 - - - +
13G LEU* 3.8 21.3 - - + -
26G LEU* 5.1 1.8 - - + -
30G ILE* 4.2 17.7 - - + -
37G ALA 2.9 19.0 + - - +
38G ALA 3.6 6.1 - - - +
40G ALA* 1.3 72.9 - - - +
42G GLN* 1.3 66.5 + - - +
44G ILE* 3.3 10.2 + - - +
45G ASN* 3.2 22.6 + - - +
156G ALA* 3.9 17.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G ALA 3.1 8.6 + - - +
39G TYR* 3.6 18.5 - - - +
41G ILE* 1.3 77.0 - - - +
43G HIS* 1.3 56.9 + - - +
45G ASN* 3.3 6.5 + - - +
46G VAL* 2.9 31.1 + - + +
79G PHE* 3.0 40.8 + - - -
81G THR* 3.0 24.3 + - - -
155G VAL 3.2 26.5 + - - +
156G ALA 3.8 8.0 + - - -
158G ASN* 3.2 33.8 + - + +
159G ALA 4.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 43 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G TYR 2.9 18.0 + - - +
40G ALA* 3.5 8.7 - - - +
42G GLN* 1.3 75.5 - - - +
44G ILE* 1.3 71.6 + - + +
46G VAL* 3.2 9.1 + - + +
47G GLN* 2.9 57.2 + - + +
220G GLU* 4.2 26.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 44 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G LYS* 4.8 10.8 - - + -
6G LEU* 4.9 10.3 - - + +
7G GLU* 3.6 41.7 - - + +
10G ALA* 3.9 20.0 - - + -
14G ARG* 4.5 9.0 - - - +
40G ALA* 2.8 36.8 + - + +
41G ILE* 3.5 10.3 - - - +
43G HIS* 1.3 76.0 - - + +
45G ASN* 1.3 58.2 + - - +
47G GLN* 3.3 6.3 + - - +
48G HIS* 2.9 27.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 45 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G ALA* 3.2 27.8 + - - +
13G LEU* 3.8 19.8 - - - +
14G ARG* 2.8 42.5 + - + +
41G ILE* 3.2 9.8 + - - +
42G GLN* 3.7 7.9 - - - +
43G HIS 3.2 0.6 - - - -
44G ILE* 1.3 78.2 - - - +
46G VAL* 1.3 63.7 + - + +
48G HIS* 3.7 3.4 - - - +
49G ASP* 3.1 30.8 + - - +
156G ALA 4.8 3.4 + - - -
158G ASN* 6.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42G GLN* 2.9 29.4 + - + +
43G HIS* 3.8 9.4 - - + +
45G ASN* 1.3 76.5 - - + +
47G GLN* 1.3 66.1 + - - +
49G ASP* 3.1 4.0 + - - +
50G VAL* 2.9 38.8 + - + +
56G VAL* 4.4 4.7 - - + -
59G ARG* 5.3 3.1 - - - +
81G THR* 3.6 38.4 - - + +
83G PHE* 4.1 22.4 - - + -
158G ASN* 4.7 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 47 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43G HIS* 2.9 49.2 + - + +
44G ILE* 3.5 7.4 - - - +
46G VAL* 1.3 83.8 - - - +
48G HIS* 1.3 61.8 + - - +
50G VAL* 3.4 19.7 + - - +
51G ALA* 3.1 22.9 + - - +
220G GLU* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 48 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G ARG* 3.7 44.8 + - - +
44G ILE* 2.9 18.2 + - + +
45G ASN* 3.7 9.0 - - - +
46G VAL 3.2 0.2 - - - -
47G GLN* 1.3 76.6 - - - +
49G ASP* 1.3 75.7 + - - +
51G ALA* 3.3 14.0 + - - +
52G GLN* 3.3 39.7 + - + +
1265G K 4.3 5.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 49 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B HIS* 3.8 12.7 - - - -
14G ARG* 4.7 3.5 - - - -
45G ASN 3.1 16.0 + - - +
46G VAL 3.7 3.6 - - - +
48G HIS* 1.3 87.9 - - - +
50G VAL* 1.3 64.8 + - - +
52G GLN* 3.0 26.3 + - - +
53G GLY 3.3 0.2 + - - -
54G ARG* 3.0 60.3 + - + +
83G PHE* 4.2 8.3 - - + -
1313G NA 3.5 18.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 50 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G VAL* 2.9 26.3 + - + +
47G GLN* 3.8 20.4 - - - +
48G HIS 3.3 0.2 - - - -
49G ASP* 1.3 75.6 - - - +
51G ALA* 1.3 58.0 + - - +
53G GLY* 2.8 20.8 + - - -
54G ARG 3.6 20.8 - - - +
56G VAL* 4.0 23.8 - - + +
83G PHE* 4.3 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 51 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47G GLN 3.1 12.8 + - - +
48G HIS* 3.5 13.2 - - - +
49G ASP 3.2 0.2 - - - -
50G VAL* 1.3 76.8 - - - +
52G GLN* 1.3 58.7 + - + +
53G GLY 3.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 3.2 31.9 + - - +
4B HIS* 4.3 9.3 + - - +
7B GLU* 3.6 42.3 - - + +
48G HIS* 3.3 33.2 + - + +
49G ASP* 3.0 26.1 + - - +
51G ALA* 1.3 77.0 - - + +
53G GLY* 1.3 59.3 + - - +
54G ARG* 3.4 2.9 + - + +
1265G K 3.8 14.3 - - - -
----------------------------------------------------------
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