Contacts of the helix formed by residues 30 - 43 (chain B) in PDB entry 2W7W
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ASN* 3.5 28.8 + - - +
25B ASP* 3.9 8.7 + - - +
26B TYR* 2.9 47.9 + - + +
29B GLY* 1.3 86.4 - - - +
31B HIS* 1.3 60.0 + - + +
32B HIS 3.6 0.4 - - - -
33B ASN* 3.4 2.0 + - - +
34B THR* 2.8 36.9 + - - +
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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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161A GLU* 3.7 8.9 + - - -
165A TYR* 2.6 32.0 + + - -
170A ASN* 3.5 27.5 - - + +
26B TYR 3.0 29.0 + - - -
27B HIS* 3.3 19.7 - - + +
30B LYS* 1.3 73.0 - - - +
32B HIS* 1.3 66.4 + - - +
34B THR* 3.1 15.8 + - - -
35B TYR* 3.2 27.6 + - + -
162B HIS* 3.4 40.0 + + + +
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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* 4.0 7.1 - - + +
6B PRO* 3.9 17.0 - - + +
27B HIS 3.0 12.8 + - - +
28B HIS* 3.4 22.8 - + - +
30B LYS 3.6 0.2 - - - -
31B HIS* 1.3 74.4 - - - +
33B ASN* 1.3 63.4 + - - +
35B TYR* 3.3 17.3 + + - +
36B VAL* 3.4 10.5 + - + +
70B GLN 4.5 0.2 - - - -
71B ILE* 3.0 39.2 + - + +
74B HIS* 3.5 24.8 - + + +
75B THR* 3.3 20.6 + - - -
78B TRP* 3.0 30.8 + + - +
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Residues in contact with ASN 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B LEU* 3.5 41.0 - - + +
28B HIS 3.4 4.4 + - - -
29B GLY 3.4 23.9 - - - +
30B LYS 3.4 1.3 + - - +
31B HIS 3.3 0.8 - - - -
32B HIS* 1.3 78.9 - - - +
34B THR* 1.3 64.8 + - - +
36B VAL* 3.0 11.9 + - - +
37B VAL* 3.0 35.5 + - - +
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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
----------------------------------------------------------
170A ASN* 5.0 5.9 + - - -
30B LYS* 2.8 28.9 + - - +
31B HIS* 3.1 8.2 + - - -
33B ASN* 1.3 75.5 + - - +
35B TYR* 1.3 60.0 + - + +
37B VAL* 3.3 8.8 + - + +
38B LYS* 2.9 56.8 + - + +
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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
----------------------------------------------------------
119A PHE* 4.2 13.8 - + - -
31B HIS* 3.2 33.3 + - + -
32B HIS* 3.6 12.1 - - - +
34B THR* 1.3 80.4 - - + +
36B VAL* 1.3 55.7 + - - +
38B LYS* 3.5 0.8 + - + -
39B LEU* 2.9 31.2 + - - +
67B ASN* 3.3 30.3 - - - +
70B GLN* 3.1 46.1 + - + -
71B ILE* 3.7 18.8 - - + +
74B HIS* 3.5 27.4 - + - -
160B TRP* 3.7 19.6 - - - -
162B HIS* 4.2 6.8 - + - -
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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 PHE* 3.3 37.7 - - + +
4B GLU* 3.9 18.2 - - - +
5B LEU* 4.1 13.0 - - - +
6B PRO* 4.7 1.8 - - + -
32B HIS* 3.6 13.2 - - + +
33B ASN* 3.0 15.6 + - - +
35B TYR* 1.3 75.1 - - - +
37B VAL* 1.3 65.2 + - + +
39B LEU* 3.2 2.8 + - - +
40B ASN* 2.9 30.0 + - - +
71B ILE* 3.7 28.0 - - + -
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ASN* 3.0 33.8 + - - +
34B THR* 3.3 11.6 + - + +
36B VAL* 1.3 75.9 - - + +
38B LYS* 1.3 67.8 + - + +
40B ASN* 3.4 8.1 + - - +
41B GLY* 3.2 18.0 + - - -
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Residues in contact with LYS 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 5.3 7.3 + - - +
117A ASN* 4.5 16.8 - - - +
34B THR* 2.9 36.5 + - + +
35B TYR* 5.7 0.4 - - + -
37B VAL* 1.3 78.4 - - + +
39B LEU* 1.3 64.6 + - - +
41B GLY* 3.1 10.5 + - - -
42B LEU* 3.2 20.2 + - + +
67B ASN* 3.4 35.4 - - - +
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Residues in contact with LEU 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.8 22.4 - - + -
35B TYR 2.9 17.9 + - - +
36B VAL 3.6 4.0 - - - +
38B LYS* 1.3 74.1 - - - +
40B ASN* 1.3 64.4 + - - +
42B LEU* 2.9 14.4 + - + -
43B ILE* 3.1 35.1 + - + +
53B LEU* 3.8 12.1 - - + -
56B ILE* 4.5 4.0 - - + -
64B VAL* 3.8 34.1 - - + +
67B ASN* 4.0 8.1 - - + +
68B ALA* 3.7 20.2 - - + +
71B ILE* 3.6 23.6 - - + -
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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
----------------------------------------------------------
2B SER* 3.7 16.3 + - - -
3B PHE* 2.9 57.1 + - - +
36B VAL* 2.9 26.2 + - - +
37B VAL* 3.7 8.0 - - - +
39B LEU* 1.3 74.8 - - - +
41B GLY* 1.3 56.8 + - - +
43B ILE* 4.1 7.6 - - - +
44B PRO* 3.0 25.9 - - - +
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Residues in contact with GLY 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 VAL 3.2 9.6 + - - -
38B LYS 3.1 6.6 + - - -
39B LEU 3.1 1.2 - - - -
40B ASN* 1.3 76.9 - - - +
42B LEU* 1.3 64.5 + - - +
43B ILE 3.5 0.2 - - - -
44B PRO* 3.5 10.0 - - - +
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Residues in contact with LEU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LYS* 3.5 12.6 - - + +
39B LEU* 2.9 8.8 + - - +
41B GLY* 1.3 82.4 - - - +
43B ILE* 1.3 63.0 + - + +
44B PRO* 3.4 2.5 - - - +
46B THR* 3.4 16.3 - - - +
63B GLY* 3.5 37.9 - - - +
64B VAL* 3.7 22.2 - - + +
67B ASN* 3.9 11.2 - - - +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 5.5 7.2 - - - +
3B PHE* 4.0 30.1 - - + -
39B LEU* 3.1 36.5 + - + +
40B ASN* 4.1 9.6 - - - +
42B LEU* 1.3 80.4 - - + +
44B PRO* 1.4 73.3 - - + +
45B GLY 3.2 0.5 + - - -
46B THR* 2.6 28.0 + - - +
48B PHE* 3.9 31.0 - - + +
49B GLU* 3.8 17.1 - - + +
50B GLY 5.6 1.1 - - - +
56B ILE* 4.7 2.0 - - + -
64B VAL* 4.7 6.5 - - + -
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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
------------------------------------------------------------
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