Contacts of the helix formed by residues 34 - 52 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K THR* 5.6 8.3 + - - +
30K ILE* 3.2 29.7 + - + +
31K GLY* 2.9 9.2 + - - +
32K ILE 3.6 0.6 - - - -
33K ASP* 1.3 72.5 - - - +
35K ALA* 1.3 65.9 + - - +
36K GLU* 3.7 9.9 + - - +
37K ALA* 3.2 30.4 + - + +
38K ALA 3.3 10.7 + - - -
152K VAL* 3.3 13.9 - - - +
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Residues in contact with ALA 35 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K ASP 3.4 7.8 + - - +
34K ASN* 1.3 71.4 - - - +
36K GLU* 1.3 66.0 + - - +
38K ALA* 3.2 3.4 + - - +
39K TYR* 3.0 36.4 + - + -
151K PHE* 3.9 28.7 - - + -
152K VAL* 4.2 4.0 - - - +
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Residues in contact with GLU 36 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34K ASN* 3.3 7.6 + - - +
35K ALA* 1.3 78.9 - - - +
37K ALA* 1.3 57.1 + - - +
39K TYR* 3.5 7.6 + - - +
40K ALA* 3.1 26.6 + - + +
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Residues in contact with ALA 37 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K THR* 5.7 2.2 - - - +
6K LEU* 4.2 24.6 - - + +
30K ILE* 4.4 10.8 - - + -
34K ASN* 3.2 33.3 + - + +
35K ALA 3.2 0.6 - - - -
36K GLU* 1.3 76.4 - - - +
38K ALA* 1.3 61.0 + - - +
40K ALA* 3.1 9.2 + - - +
41K ILE* 2.9 34.2 + - - +
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Residues in contact with ALA 38 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE* 4.5 5.7 - - + +
34K ASN 3.3 2.6 + - - -
35K ALA* 3.2 10.0 + - - +
37K ALA* 1.3 77.2 - - - +
39K TYR* 1.3 61.2 + - - +
41K ILE* 3.3 2.9 + - - +
42K GLN* 3.1 18.2 + - - +
152K VAL* 3.4 42.8 - - + +
155K VAL* 3.7 17.3 - - + -
156K ALA* 3.4 18.6 + - - +
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Residues in contact with TYR 39 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K ALA* 3.0 30.7 + - + +
36K GLU* 3.9 5.6 - - - +
38K ALA* 1.3 75.8 - - - +
40K ALA* 1.3 57.7 + - - +
42K GLN* 3.4 10.3 + - - +
43K HIS* 2.9 29.0 + - - +
77K PRO 4.3 4.5 + - - -
78K ASP* 3.8 11.3 + - - -
79K PHE* 3.2 72.1 + + - -
151K PHE* 4.4 15.1 - + - -
155K VAL* 3.4 25.2 - - + +
210K TRP* 4.3 4.0 - - - -
214K LYS* 4.2 18.6 + - - -
218K LEU* 6.1 2.2 - - + -
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Residues in contact with ALA 40 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LEU* 4.0 19.5 - - + -
36K GLU* 3.1 16.7 + - + +
37K ALA* 3.1 10.3 + - - +
39K TYR* 1.3 74.6 - - - +
41K ILE* 1.3 58.6 + - - +
43K HIS* 3.2 8.6 + - - +
44K ILE* 2.8 38.9 + - + +
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Residues in contact with ILE 41 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LEU* 3.9 23.8 - - + +
9K LEU* 3.9 31.2 - - + -
10K ALA* 3.8 16.8 - - - +
13K LEU* 3.8 27.6 - - + -
26K LEU* 5.0 1.6 - - + -
30K ILE* 4.2 17.7 - - + -
37K ALA 2.9 17.8 + - - +
38K ALA 3.3 6.7 + - - +
40K ALA* 1.3 72.6 - - - +
42K GLN* 1.3 65.8 + - - +
44K ILE* 3.2 10.8 + - - +
45K ASN* 3.2 23.7 + - - +
156K ALA* 3.9 17.7 - - + +
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Residues in contact with GLN 42 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38K ALA 3.1 9.4 + - - +
39K TYR* 3.6 16.7 - - - +
40K ALA 3.4 0.2 - - - -
41K ILE* 1.3 75.5 - - - +
43K HIS* 1.3 58.6 + - - +
45K ASN* 3.3 4.8 + - - +
46K VAL* 2.9 30.8 + - + +
79K PHE* 3.0 40.8 + - - -
81K THR* 3.1 23.9 + - - -
155K VAL 3.2 26.0 + - - +
156K ALA 3.8 7.8 + - - -
158K ASN* 3.2 35.4 + - + +
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Residues in contact with HIS 43 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K TYR 2.9 18.3 + - - +
40K ALA* 3.4 9.4 - - - +
41K ILE 3.2 0.2 - - - -
42K GLN* 1.3 74.7 - - - +
44K ILE* 1.3 69.4 + - + +
46K VAL* 3.3 9.5 + - + +
47K GLN* 2.9 58.7 + - + +
220K GLU* 4.2 26.8 + - - -
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Residues in contact with ILE 44 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K LYS* 4.8 10.3 - - + -
6K LEU* 4.9 10.5 - - + +
7K GLU* 3.6 42.8 - - + +
10K ALA* 3.8 19.3 - - + -
14K ARG* 4.5 6.7 - - - +
40K ALA* 2.8 37.7 + - + +
41K ILE* 3.5 9.9 - - - +
43K HIS* 1.3 77.0 - - + +
45K ASN* 1.3 60.3 + - - +
47K GLN* 3.3 7.1 + - - +
48K HIS* 2.9 28.3 + - + +
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Residues in contact with ASN 45 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K ALA* 3.2 28.0 + - - +
13K LEU* 3.8 19.6 - - - +
14K ARG* 2.8 42.2 + - + +
41K ILE* 3.2 11.4 + - - +
42K GLN* 3.8 7.9 - - - +
44K ILE* 1.3 77.1 - - - +
46K VAL* 1.3 65.4 + - + +
48K HIS* 3.5 3.6 + - - +
49K ASP* 3.1 32.0 + - - +
156K ALA 4.8 3.6 + - - -
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Residues in contact with VAL 46 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42K GLN* 2.9 30.0 + - + +
43K HIS* 3.8 10.1 - - - +
45K ASN* 1.3 74.7 - - - +
47K GLN* 1.3 63.7 + - - +
49K ASP* 3.2 3.3 + - - +
50K VAL* 2.9 39.7 + - + +
56K VAL* 4.4 5.2 - - + -
59K ARG* 5.3 3.1 - - - +
81K THR* 3.6 38.6 - - + +
83K PHE* 4.0 23.6 - - + -
158K ASN* 4.7 3.6 - - - +
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Residues in contact with GLN 47 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43K HIS* 2.9 49.7 + - + +
44K ILE* 3.5 6.7 - - - +
46K VAL* 1.3 82.7 - - - +
48K HIS* 1.3 62.8 + - - +
50K VAL* 3.5 19.2 + - - +
51K ALA* 3.1 23.2 + - - +
220K GLU* 5.3 0.7 - - - +
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Residues in contact with HIS 48 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14K ARG* 3.7 43.0 + - - +
44K ILE* 2.9 18.4 + - + +
45K ASN* 3.6 9.2 - - - +
47K GLN* 1.3 76.5 - - - +
49K ASP* 1.3 75.0 + - - +
51K ALA* 3.3 16.4 + - - +
52K GLN* 3.3 37.0 + - + +
1265K K 4.2 5.3 - - - -
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Residues in contact with ASP 49 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I HIS* 3.5 12.1 - - - -
14K ARG* 4.8 1.6 - - - -
45K ASN 3.1 17.2 + - - +
46K VAL 3.7 3.6 - - - +
48K HIS* 1.3 89.2 - - - +
50K VAL* 1.3 64.3 + - - +
52K GLN* 3.0 23.6 + - - +
53K GLY 3.4 0.2 + - - -
54K ARG* 3.0 60.0 + - + +
83K PHE* 4.1 9.2 - - + -
1265K K 4.0 6.8 - - - -
1305K NA 3.4 16.8 - - - -
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Residues in contact with VAL 50 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46K VAL* 2.9 26.5 + - + +
47K GLN* 3.8 20.0 - - - +
48K HIS 3.4 0.2 - - - -
49K ASP* 1.3 75.9 - - - +
51K ALA* 1.3 57.5 + - - +
53K GLY* 2.8 21.7 + - - -
54K ARG 3.6 19.9 - - - +
56K VAL* 4.0 24.7 - - + -
83K PHE* 4.3 2.5 - - + -
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Residues in contact with ALA 51 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47K GLN 3.1 13.2 + - - +
48K HIS* 3.4 13.2 - - - +
49K ASP 3.2 0.2 - - - -
50K VAL* 1.3 76.6 - - - +
52K GLN* 1.3 59.9 + - + +
53K GLY 3.3 1.2 + - - -
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Residues in contact with GLN 52 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I LYS* 2.7 36.5 + - - +
4I HIS* 4.6 6.5 + - - +
7I GLU* 3.2 45.2 - - + +
48K HIS* 3.3 32.3 + - + +
49K ASP* 3.0 21.2 + - - +
51K ALA* 1.3 77.4 - - + +
53K GLY* 1.3 57.4 + - - +
54K ARG* 3.4 2.9 + - + +
1265K K 3.6 20.1 - - - -
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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) + - + + + + + -
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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