Contacts of the helix formed by residues 30 - 44 (chain B) in PDB entry 2AW9
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 LYS 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.8 32.8 - - + +
25B GLU* 6.4 0.2 - - - -
26B ILE* 2.8 31.9 + - + +
29B THR* 1.3 97.3 - - - +
31B HIS* 1.3 62.3 + - - +
32B HIS 3.5 0.9 - - - -
33B GLN* 3.6 2.4 - - - +
34B THR* 2.7 33.5 + - - +
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Residues in contact with HIS 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A GLU* 3.7 22.9 - - - -
180A TYR* 2.7 31.4 + + - -
185A ASN* 3.5 24.3 - - + +
26B ILE* 3.2 16.9 + - + -
27B HIS* 3.3 25.1 - - + +
30B LYS* 1.3 80.4 - - - +
32B HIS* 1.3 64.9 + - - +
34B THR* 3.3 4.9 + - - -
35B TYR* 3.1 39.0 + - + -
177B HIS* 3.6 26.0 + + + +
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Residues in contact with HIS 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.4 9.1 - - + +
6B PRO* 3.6 18.1 - - + +
27B HIS* 2.9 13.0 + - - +
28B HIS* 3.3 15.3 - - - +
31B HIS* 1.3 74.9 - - - +
33B GLN* 1.3 65.9 + - - +
34B THR 3.0 0.9 + - - -
35B TYR* 3.0 18.0 + - + +
36B VAL* 3.1 16.1 + - + +
77B GLY 4.5 1.1 - - - -
78B HIS* 2.7 40.5 + - - -
81B HIS* 3.4 16.9 - - + +
82B SER* 3.4 32.5 - - - -
85B TRP* 3.0 22.6 + - + -
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Residues in contact with GLN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B LEU* 3.3 36.0 - - - +
28B HIS 3.3 5.0 + - - +
29B THR 3.0 28.2 - - - +
30B LYS* 3.4 4.5 + - - +
31B HIS 3.3 0.2 - - - -
32B HIS* 1.3 77.4 - - - +
34B THR* 1.3 58.2 + - - +
36B VAL* 3.2 12.6 + - - +
37B ASP* 2.8 67.0 + - - +
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Residues in contact with THR 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LYS* 2.7 22.8 + - - +
31B HIS* 3.5 6.3 - - - -
32B HIS 3.1 0.2 - - - -
33B GLN* 1.3 72.7 - - - +
35B TYR* 1.3 60.9 + - + +
36B VAL 3.0 1.3 - - - -
37B ASP* 4.3 8.2 + - + -
38B ASN* 2.7 61.8 + - - +
74B ASN* 5.4 0.4 - - - +
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Residues in contact with TYR 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A PHE* 3.6 27.6 - + - -
31B HIS* 3.1 34.6 + - + -
32B HIS* 3.0 7.9 + - - +
34B THR* 1.3 79.7 - - + +
36B VAL* 1.3 57.3 + - - +
39B ALA* 3.0 31.4 + - - +
73B ASN 4.1 8.3 - - - -
74B ASN* 3.3 34.9 - - - +
77B GLY* 3.7 5.8 - - - -
78B HIS* 3.8 10.8 - - - +
81B HIS* 3.5 22.9 - + - -
152B GLN* 3.0 31.0 + - + -
175B TRP* 3.5 22.5 - - - -
177B HIS* 4.3 4.8 - + - -
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.5 31.5 - - + +
4B THR* 4.0 14.1 - - - -
5B LEU* 4.2 8.1 - - + +
32B HIS* 3.1 19.7 + - + +
33B GLN* 3.3 14.6 - - - +
34B THR 3.0 0.6 - - - -
35B TYR* 1.3 74.0 - - - +
37B ASP* 1.3 72.5 + - - +
39B ALA* 3.1 5.7 + - - +
40B ASN* 2.9 27.9 + - - +
78B HIS* 3.4 39.9 - - + +
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Residues in contact with ASP 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLN* 2.8 51.1 + - - +
34B THR* 3.8 7.9 + - + +
36B VAL* 1.3 75.6 - - - +
38B ASN* 1.3 59.7 + - - +
40B ASN* 3.3 10.1 + - - +
41B LYS* 3.0 49.8 + - - +
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Residues in contact with ASN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B THR* 2.7 41.8 + - - +
37B ASP* 1.3 72.5 - - - +
39B ALA* 1.3 64.1 + - - +
41B LYS* 3.3 29.1 + - - +
42B ALA* 3.2 20.4 + - - +
70B ALA* 5.6 0.7 - - - +
74B ASN* 3.3 30.2 + - - +
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Residues in contact with ALA 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B TYR* 4.0 22.9 - - + -
35B TYR 3.0 19.1 + - - +
36B VAL* 3.6 3.6 - - - +
38B ASN* 1.3 75.6 - - - +
40B ASN* 1.3 60.2 + - - +
42B ALA* 2.9 8.6 + - - +
43B LEU* 2.8 34.4 + - - +
71B LEU* 4.9 4.0 - - + -
74B ASN* 3.6 6.6 - - - +
75B ALA* 3.9 23.3 - - + +
78B HIS* 5.5 0.7 - - + -
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Residues in contact with ASN 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ALA* 3.3 30.2 - - + +
2B ALA* 3.5 4.9 + - - +
3B TYR* 2.8 50.5 + - - +
36B VAL* 2.9 22.2 + - - +
37B ASP* 3.3 12.5 + - - +
39B ALA* 1.3 76.3 - - - +
41B LYS* 1.3 61.6 + - + +
43B LEU* 3.3 13.8 + - - +
44B GLU* 3.3 16.1 + - - +
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Residues in contact with LYS 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B ASP* 3.0 32.8 + - - +
38B ASN* 3.3 30.8 + - - +
39B ALA 3.2 0.2 - - - -
40B ASN* 1.3 76.1 - - - +
42B ALA* 1.3 63.8 + - - +
44B GLU* 3.0 27.8 - - - +
67B LYS* 4.7 1.9 + - - -
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASN 3.2 10.7 + - - +
39B ALA* 2.9 10.3 + - - +
41B LYS* 1.3 76.8 - - - +
43B LEU* 1.3 59.3 + - - +
44B GLU 2.9 4.4 + - - -
46B THR* 3.8 2.3 - - - +
67B LYS* 2.7 42.9 + - + +
70B ALA* 4.2 19.1 - - + -
71B LEU* 3.5 27.8 - - + +
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Residues in contact with LEU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ALA* 6.5 0.2 - - + -
2B ALA* 3.5 21.5 - - + +
3B TYR* 3.4 38.1 - - + +
39B ALA 2.8 21.7 + - - +
40B ASN* 3.7 6.7 - - - +
42B ALA* 1.3 68.4 - - - +
44B GLU* 1.3 62.6 - - - +
45B GLY 3.4 0.9 - - - -
46B THR* 2.9 32.4 + - - +
48B PHE* 4.0 18.6 - - + +
49B ALA* 3.8 24.4 - - + +
56B LEU* 3.8 12.6 - - + -
71B LEU* 3.7 24.5 - - + -
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASN 3.3 15.8 + - - +
41B LYS* 3.0 24.8 - - - +
42B ALA 2.9 2.2 + - - +
43B LEU* 1.3 77.3 - - - +
45B GLY* 1.3 58.5 + - - +
46B THR 3.1 5.4 + - - +
67B LYS* 5.0 0.9 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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