Contacts of the helix formed by residues 23 - 36 (chain B) in PDB entry 1W5A
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 23 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A LYS* 6.0 0.2 - - - -
22B LEU* 1.3 73.6 - - - +
24B PRO* 1.3 75.2 - - - +
25B GLU* 3.4 9.7 + - - +
26B ASP* 2.9 34.2 + - - +
27B LYS* 2.9 22.6 + - - +
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Residues in contact with PRO 24 (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 LEU 3.9 2.7 - - - +
23B SER* 1.3 87.4 - - - +
25B GLU* 1.3 62.0 + - + +
27B LYS* 3.4 13.3 + - + +
28B GLU* 3.2 22.9 + - - +
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Residues in contact with GLU 25 (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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81A ALA 4.6 4.3 - - - +
82A ASP 4.6 2.3 - - - +
83A LYS* 3.3 23.3 - - - +
84A LYS* 2.8 66.0 + - + +
23B SER* 3.1 9.4 + - - +
24B PRO* 1.3 83.9 - - + +
26B ASP* 1.3 63.8 + - - +
28B GLU* 3.5 12.8 + - - +
29B LEU* 3.4 23.8 + - + +
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Residues in contact with ASP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.5 26.4 - - + +
80A LYS* 5.5 4.5 + - - -
84A LYS* 2.6 37.0 + - - +
22B LEU* 4.4 18.8 - - + +
23B SER* 2.9 28.3 + - - +
25B GLU* 1.3 78.3 - - - +
27B LYS* 1.3 59.5 + - - +
29B LEU* 3.0 9.8 + - - +
30B LEU* 2.8 29.8 + - - +
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Residues in contact with LYS 27 (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 LEU* 3.8 31.4 - - + +
23B SER 2.9 16.5 + - - +
24B PRO* 3.7 13.9 - - + +
25B GLU 3.4 0.2 - - - -
26B ASP* 1.3 75.4 - - - +
28B GLU* 1.3 62.9 + - - +
30B LEU* 3.0 14.2 + - - +
31B GLU* 3.0 23.2 + - - +
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Residues in contact with GLU 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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89A LYS* 5.5 8.0 + - - -
24B PRO 3.2 10.4 + - - +
25B GLU* 3.6 14.9 - - - +
27B LYS* 1.3 78.6 - - - +
29B LEU* 1.3 59.1 + - + +
31B GLU* 3.5 8.2 + - - +
32B TYR* 3.0 27.7 + - + +
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ALA* 4.3 14.1 - - + +
76A LEU* 4.2 17.5 - - + -
77A ILE* 3.9 37.7 - - + +
84A LYS* 4.3 14.1 - - + -
86A LEU* 4.0 37.7 - - + -
89A LYS* 6.0 0.7 - - - +
25B GLU* 3.4 14.5 + - + +
26B ASP* 3.0 11.1 + - - +
28B GLU* 1.3 78.8 - - + +
30B LEU* 1.3 59.3 + - - +
32B TYR* 3.3 5.9 + - + +
33B LEU* 2.8 34.8 + - + +
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Residues in contact with LEU 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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77A ILE* 3.5 25.3 - - + +
22B LEU* 3.3 31.9 - - + -
26B ASP 2.8 9.1 + - - +
27B LYS* 3.0 12.5 + - + +
29B LEU* 1.3 76.7 - - - +
31B GLU* 1.3 57.9 + - - +
33B LEU* 3.3 9.4 + - + +
34B GLN* 3.0 33.9 + - - +
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Residues in contact with GLU 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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27B LYS 3.0 14.5 + - - +
28B GLU* 4.0 7.1 - - - +
30B LEU* 1.3 73.1 - - - +
32B TYR* 1.3 66.7 + - - +
34B GLN* 3.9 11.3 - - + +
35B GLN* 3.0 38.6 + - + +
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Residues in contact with TYR 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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73A ALA* 4.4 8.3 - - + -
86A LEU* 4.0 22.0 - - + -
89A LYS* 3.7 22.4 + - + -
93A ARG* 2.9 32.3 - - + +
94A GLY* 3.1 26.5 + - - -
28B GLU* 3.0 18.4 + - + +
29B LEU* 3.4 8.7 - - + +
31B GLU* 1.3 77.5 - - - +
33B LEU* 1.3 51.2 + - + +
35B GLN* 3.1 19.3 + - - +
36B THR* 2.5 60.8 + - - -
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Residues in contact with LEU 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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73A ALA* 3.7 25.8 - - + +
74A GLN* 4.0 41.7 - - + +
77A ILE* 4.3 24.9 - - + -
94A GLY 4.9 4.3 - - - +
95A LEU* 6.4 1.1 - - + -
29B LEU 2.8 23.5 + - - +
30B LEU* 3.3 11.2 + - + +
32B TYR* 1.3 73.9 - - + +
34B GLN* 1.3 58.9 + - - +
36B THR* 2.9 34.5 + - + +
37B LYS* 3.8 0.5 + - - -
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Residues in contact with GLN 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 LEU* 3.0 19.6 + - - +
31B GLU* 3.9 11.8 - - - +
33B LEU* 1.3 76.2 - - - +
35B GLN* 1.3 59.2 + - - +
37B LYS* 3.1 43.5 + - - +
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Residues in contact with GLN 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 GLU* 3.0 32.2 + - + +
32B TYR* 3.5 19.2 - - - +
34B GLN* 1.3 71.9 - - - +
36B THR* 1.3 56.2 + - - +
37B LYS* 2.9 21.2 + - - +
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Residues in contact with THR 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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93A ARG* 3.4 32.5 - - + +
94A GLY* 5.3 0.9 - - - -
95A LEU* 5.0 11.0 - - + -
32B TYR* 2.5 48.9 + - + -
33B LEU* 2.9 19.6 + - + -
35B GLN* 1.3 71.8 - - - +
37B LYS* 1.3 66.8 + - - +
38B ALA* 3.2 4.9 + - - +
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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