Contacts of the helix formed by residues 27 - 37 (chain B) in PDB entry 2JWN
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 SER 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B LEU* 1.3 79.9 - - - +
28B ALA* 1.3 65.2 + - - +
29B GLU* 4.3 2.7 - - - -
30B GLU* 2.8 37.8 + - - +
31B LYS* 3.0 21.7 + - - +
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Residues in contact with ALA 28 (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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26B LEU 3.5 1.9 + - - -
27B SER* 1.3 72.8 - - - +
29B GLU* 1.3 64.1 + - + +
31B LYS* 3.2 10.8 + - - +
32B LYS* 3.0 31.2 + - + +
116B MET* 3.8 25.6 - - + -
119B ILE* 5.8 7.9 - - + -
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Residues in contact with GLU 29 (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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27B SER* 3.2 3.1 - - - -
28B ALA* 1.3 77.7 - - + +
30B GLU* 1.4 65.4 + - - +
31B LYS 3.0 1.8 - - - -
32B LYS* 3.1 13.3 + - + +
33B GLU* 2.9 37.7 + - + +
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Residues in contact with GLU 30 (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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73A PHE* 4.2 19.3 - - + -
26B LEU* 3.7 17.7 - - + -
27B SER* 2.8 35.6 + - - +
29B GLU* 1.4 78.0 - - - +
31B LYS* 1.3 58.8 + - - +
33B GLU* 3.6 4.9 + - - +
34B ILE* 3.1 33.6 + - - +
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Residues in contact with LYS 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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16B GLY 2.9 19.0 + - - -
17B ALA* 3.5 35.1 + - + +
20B GLU* 2.6 30.6 + - - -
25B PRO* 3.7 9.6 - - - -
26B LEU* 3.4 34.6 - - + +
27B SER 3.0 12.2 + - - +
28B ALA* 3.2 14.6 - - - +
29B GLU 3.0 0.2 - - - -
30B GLU* 1.3 76.4 - - - +
32B LYS* 1.3 72.9 + - - +
34B ILE* 3.1 23.7 - - + +
35B ASP* 2.8 17.2 + - - +
65B ARG* 5.4 4.4 - - - +
114B THR* 5.5 3.4 - - + -
116B MET* 5.0 1.3 - - + -
119B ILE* 6.0 1.6 - - + -
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Residues in contact with LYS 32 (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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17B ALA* 5.4 1.1 - - - -
28B ALA* 3.0 22.4 + - + +
29B GLU* 3.1 18.1 + - + +
31B LYS* 1.3 81.7 - - - +
33B GLU* 1.3 64.9 + - - +
35B ASP* 2.7 32.4 + - - +
36B LYS* 3.0 36.4 + - + +
113B ARG* 4.6 5.3 - - - +
114B THR 2.9 18.6 + - - -
115B ASN* 4.4 7.1 + - - +
116B MET* 3.7 28.3 - - + -
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Residues in contact with GLU 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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29B GLU* 2.9 21.5 + - + +
30B GLU* 4.1 5.4 - - - +
32B LYS* 1.3 78.6 - - + +
34B ILE* 1.3 60.1 + - + +
36B LYS* 2.8 40.9 + - - +
37B ARG* 3.0 68.3 + - - +
88B ARG* 5.4 3.3 - - - +
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Residues in contact with ILE 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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73A PHE* 3.5 38.1 - - + -
26B LEU* 4.8 0.9 - - + -
30B GLU 3.1 19.8 + - - +
31B LYS* 3.1 27.1 - - + +
33B GLU* 1.3 75.7 - - + +
35B ASP* 1.4 58.0 + - - +
37B ARG* 3.2 14.2 + - - +
38B SER* 2.9 28.1 + - - -
64B ASN* 4.0 18.4 - - + +
65B ARG* 3.7 20.9 - - - +
84B GLU* 3.8 25.3 - - + +
85B PHE 4.6 6.1 - - - +
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Residues in contact with ASP 35 (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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31B LYS 2.8 19.3 + - - +
32B LYS* 2.7 34.4 + - - +
34B ILE* 1.4 70.4 - - - +
36B LYS* 1.3 60.1 + - + +
37B ARG 3.0 4.5 - - - -
38B SER* 2.8 20.9 + - - +
84B GLU* 4.8 0.9 - - - -
111B PRO* 5.5 1.4 - - - +
112B LYS* 2.7 53.3 + - - +
113B ARG* 3.4 14.1 - - + -
114B THR* 2.7 31.5 + - - +
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Residues in contact with LYS 36 (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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32B LYS* 3.1 23.3 - - + +
33B GLU* 2.8 40.0 + - - +
35B ASP* 1.3 80.9 - - + +
37B ARG* 1.3 57.9 + - - +
38B SER 3.4 0.7 - - - -
88B ARG* 2.7 48.3 + - - +
91B VAL* 3.5 6.1 - - - +
111B PRO* 5.8 1.5 - - - +
113B ARG* 5.9 5.8 - - - +
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Residues in contact with ARG 37 (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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33B GLU* 3.0 55.4 + - - +
34B ILE* 3.2 10.7 + - - +
35B ASP 3.0 0.6 - - - -
36B LYS* 1.3 77.9 - - - +
38B SER* 1.3 58.8 + - - +
64B ASN* 5.3 2.8 - - - +
85B PHE* 2.9 56.1 + - - +
86B ALA* 3.0 34.4 + - - +
87B GLU* 3.9 6.0 - - - +
88B ARG* 3.9 27.7 - - + +
91B VAL* 3.5 13.4 - - - +
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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