Contacts of the helix formed by residues 25 - 36 (chain A) in PDB entry 2W83
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 GLY 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ALA 3.2 0.6 - - - -
24A ALA* 1.3 79.0 - - - +
26A LYS* 1.3 66.9 + - - +
28A THR* 3.4 2.8 + - - -
29A ILE* 3.0 28.1 + - - +
87A VAL* 4.3 5.6 - - - -
122A ASN* 3.9 2.9 - - - -
156A ALA* 4.3 0.3 - - - +
1173A GTP 3.0 41.7 + - - -
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Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 3.2 31.7 - - + +
19A LEU* 3.3 31.4 - - - +
20A GLY* 3.0 13.1 + - - +
21A LEU 3.0 21.0 + - - -
24A ALA* 3.8 1.3 - - + -
25A GLY* 1.3 75.2 - - - +
27A THR* 1.3 58.4 + - - +
29A ILE* 3.2 2.6 + - - +
30A LEU 3.0 23.0 + - - -
63A ASP* 3.3 12.3 - - - +
64A VAL 3.2 25.4 - - - -
66A GLY 4.0 0.4 - - - +
87A VAL* 3.8 25.1 - - + +
1173A GTP 2.7 45.8 + - - +
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS* 1.3 71.7 - - - +
28A THR* 1.3 65.7 + - - +
30A LEU* 3.3 2.5 + - - -
31A TYR* 3.1 39.0 + - + +
39A VAL* 5.5 0.2 - - + -
41A THR* 3.7 22.2 - - + -
42A ILE 5.6 0.7 - - - +
44A THR* 2.9 4.4 + - - +
48A ASN* 3.6 19.7 - - - +
63A ASP* 2.5 18.8 + - - +
1173A GTP 3.0 9.7 + - - -
1174A MG 2.1 31.0 - - - -
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Residues in contact with THR 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLY 3.6 5.4 - - - -
26A LYS 3.3 0.2 - - - -
27A THR* 1.3 76.5 - - - +
29A ILE* 1.3 56.3 + - - +
31A TYR* 3.8 0.5 - - - +
32A LYS* 2.9 31.9 + - - +
37A GLN 4.8 1.0 - - - +
38A SER* 4.1 21.9 - - - +
39A VAL* 4.7 8.8 + - - +
41A THR* 4.1 12.6 - - - +
156A ALA* 3.7 28.9 - - + +
157A THR* 4.2 3.6 - - + +
1173A GTP 2.8 51.1 + - + +
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Residues in contact with ILE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 4.2 13.0 - - + -
25A GLY 3.0 17.9 + - - +
26A LYS 3.5 7.0 - - - +
28A THR* 1.3 73.4 - - - +
30A LEU* 1.3 67.4 + - - +
32A LYS* 3.3 1.4 + - - +
33A LEU* 3.0 41.7 + - + +
85A ILE* 6.0 0.7 - - + -
87A VAL* 3.8 26.9 - - + -
120A PHE* 3.7 35.7 - - + -
122A ASN* 4.5 4.5 - - - -
156A ALA* 3.5 19.3 - - + -
162A LEU* 3.9 25.5 - - + +
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Residues in contact with LEU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 3.9 7.6 - - + -
26A LYS 3.0 14.0 + - - +
27A THR* 3.3 9.4 + - - +
29A ILE* 1.3 77.7 - - - +
31A TYR* 1.3 73.7 + - + +
33A LEU* 3.4 7.5 + - + +
34A LYS* 2.8 28.2 + - - +
48A ASN* 3.7 34.3 - - + +
50A GLU* 3.9 26.0 - - + -
52A VAL* 4.7 5.8 - - + -
61A VAL* 3.7 35.2 - - + +
63A ASP* 3.7 15.0 - - + +
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Residues in contact with TYR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 3.1 36.0 + - + +
28A THR 4.5 0.2 - - - +
30A LEU* 1.3 89.0 - - + +
32A LYS* 1.3 61.4 + - - +
33A LEU 3.3 0.4 - - - -
34A LYS* 4.2 7.0 - - + +
35A LEU* 2.8 55.0 + - + +
36A GLY 3.4 0.2 + - - -
37A GLN 3.4 6.4 - - - +
39A VAL* 3.8 31.2 - - + -
48A ASN* 3.6 23.0 + - + +
49A VAL 4.7 0.3 + - - -
50A GLU* 2.8 45.2 + - + +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A THR* 2.9 19.5 + - + +
29A ILE 3.7 3.6 - - - +
31A TYR* 1.3 77.6 - - - +
33A LEU* 1.3 57.7 + - - +
36A GLY* 2.9 46.1 + - - -
37A GLN* 3.4 26.1 + - - +
38A SER 4.1 1.9 - - - +
156A ALA 3.4 20.9 - - - +
157A THR 3.7 12.6 + - - +
158A SER* 3.4 28.7 + - - +
159A GLY* 3.6 5.8 - - - +
162A LEU* 3.8 17.3 - - + -
163A TYR* 4.6 6.1 + - + -
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Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A MET* 6.3 0.2 - - + -
29A ILE* 3.0 36.4 + - + +
30A LEU* 3.6 6.5 - - + +
32A LYS* 1.3 80.3 - - - +
34A LYS* 1.3 62.8 + - - +
36A GLY* 4.1 2.1 + - - -
52A VAL* 4.2 23.7 - - + +
61A VAL* 5.6 8.3 - - + -
85A ILE* 6.0 3.6 - - + -
120A PHE* 5.7 2.2 - - + -
162A LEU* 3.8 28.5 - - + +
163A TYR* 3.6 43.7 + - + -
166A LEU* 3.9 30.5 - - + -
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Residues in contact with LYS 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A LEU 2.8 20.6 + - - +
31A TYR* 4.3 11.0 - - + -
33A LEU* 1.3 77.3 - - - +
35A LEU* 1.3 74.7 + - + +
50A GLU* 3.8 36.8 + - + +
51A THR* 2.9 32.7 + - - +
52A VAL* 4.2 9.6 - - + +
432D ASP* 4.2 13.5 + - - +
435D GLN* 4.4 13.7 + - - +
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A TYR* 2.8 39.0 + - + +
34A LYS* 1.3 88.9 - - + +
36A GLY* 1.3 60.2 + - - +
37A GLN* 3.1 35.8 + - + +
39A VAL* 4.1 20.6 - - + -
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Residues in contact with GLY 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 2.9 38.0 + - - -
33A LEU 4.1 1.8 + - - -
34A LYS 3.6 1.0 - - - -
35A LEU* 1.3 77.4 - - - +
37A GLN* 1.3 62.5 + - - +
163A TYR* 5.9 1.1 - - - -
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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