Contacts of the helix formed by residues 37 - 44 (chain B) in PDB entry 2W7N
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 GLN 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL* 3.9 27.1 - - + +
35B LYS 3.6 1.2 + - - -
36B PRO* 1.3 71.6 - - - +
38B ALA* 1.3 62.7 + - - +
40B PHE* 3.0 13.8 + - - -
41B ALA* 3.1 10.5 + - - +
48B ARG 4.4 2.6 - - - +
51B VAL* 3.5 21.6 - - + +
52B SER* 3.2 38.3 + - - +
55B VAL* 3.9 23.7 - - + +
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Residues in contact with ALA 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B PRO* 3.1 10.9 - - + +
37B GLN* 1.3 77.6 - - - +
39B THR* 1.3 61.5 + - - +
41B ALA* 3.3 9.4 + - - +
42B THR* 3.1 29.4 + - - +
48B ARG* 6.2 4.5 - - - -
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B LYS* 4.9 8.7 - - + +
36B PRO* 3.2 31.8 + - - +
37B GLN 3.1 0.6 + - - -
38B ALA* 1.3 78.1 - - - +
40B PHE* 1.3 70.0 + - + +
42B THR* 3.9 4.5 - - - -
43B SER* 3.0 31.9 + - - +
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Residues in contact with PHE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 3.8 36.1 - - + -
26B ILE* 4.1 31.6 - - + -
29B GLY* 3.7 37.2 - - - -
30B VAL* 4.2 11.0 - - + -
35B LYS* 4.1 27.6 - - + -
36B PRO 3.8 12.3 - - - -
37B GLN 3.0 7.2 + - - +
39B THR* 1.3 82.9 - - + +
41B ALA* 1.3 64.4 + - - +
42B THR 3.2 1.6 - - - -
43B SER* 3.5 11.9 - - - -
44B LEU* 3.0 32.6 + - + +
51B VAL* 4.1 9.9 - - + +
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Residues in contact with ALA 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 GLN 3.1 10.4 + - - +
38B ALA* 3.3 12.3 + - - +
40B PHE* 1.3 75.0 - - - +
42B THR* 1.3 58.6 + - - +
45B GLY* 3.1 9.5 + - - -
46B LEU 3.0 43.4 + - - +
47B THR 4.5 6.3 - - - +
48B ARG* 4.6 13.2 - - + +
51B VAL* 3.6 18.3 - - + +
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Residues in contact with THR 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 ALA* 3.1 17.2 + - - +
39B THR* 3.9 4.9 - - - -
41B ALA* 1.3 77.8 - - - +
43B SER* 1.3 66.4 + - - +
44B LEU 3.3 0.7 + - - -
45B GLY* 3.5 7.4 + - - -
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Residues in contact with SER 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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25B GLU* 5.1 1.7 + - - -
39B THR* 3.0 24.3 + - - +
40B PHE* 3.5 16.8 - - - -
42B THR* 1.3 78.0 - - - +
44B LEU* 1.3 72.0 + - - +
45B GLY 3.9 0.2 + - - -
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Residues in contact with LEU 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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22B GLN* 3.7 29.6 + - + +
25B GLU* 4.1 20.6 - - - +
26B ILE* 3.5 38.8 - - + -
40B PHE* 3.0 26.9 + - + +
43B SER* 1.3 88.2 - - - +
45B GLY* 1.3 65.3 + - - +
46B LEU* 4.0 16.6 - - + +
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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