Contacts of the helix formed by residues 33 - 43 (chain A) in PDB entry 1W57
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 LEU 33 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A LYS* 3.3 30.7 - - + +
24A GLN* 3.1 15.4 + - + +
26A LEU* 2.8 22.4 + - + +
28A LEU* 4.3 15.3 - - + -
31A ASP 3.8 0.6 + - - -
32A PRO* 1.3 68.8 - - - +
34A TRP* 1.3 66.1 + - - +
36A TYR* 3.2 8.8 + - - +
37A ALA* 2.8 26.7 + - - +
97A VAL* 4.0 27.8 - - + +
98A ALA* 4.2 6.1 - - - +
100A VAL* 3.9 19.4 - - + +
192A LEU* 3.5 29.2 - - + -
203A LEU* 5.0 0.2 - - + -
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Residues in contact with TRP 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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10A ALA* 4.2 13.0 - - + -
24A GLN* 3.0 40.2 + - + -
25A PHE* 3.7 19.2 - + - -
32A PRO* 3.1 14.8 + - + +
33A LEU* 1.3 77.9 - - - +
35A LEU* 1.3 92.7 + - + +
37A ALA* 3.8 2.3 - - - +
38A THR* 2.6 41.0 + - - -
52A VAL* 4.4 8.5 - - + -
60A MET* 3.4 63.8 - - + +
63A PHE* 3.9 21.4 - + + -
64A THR* 4.6 2.9 - - + -
67A TYR* 4.7 7.0 - + - -
69A PHE* 3.8 27.4 - + - -
97A VAL* 3.9 12.5 - - + +
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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 ASP* 3.7 22.2 - - + +
32A PRO* 2.9 14.8 + - + +
34A TRP* 1.3 102.5 - - + +
36A TYR* 1.3 57.9 + - - +
37A ALA 3.2 1.1 - - - -
38A THR* 4.2 1.6 - - - -
39A LYS* 2.7 61.9 + - + +
63A PHE* 4.1 31.4 - - + +
64A THR* 4.6 7.9 - - - +
66A ASN* 6.2 0.2 - - - +
67A TYR* 3.7 31.0 - - + +
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Residues in contact with TYR 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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28A LEU* 3.5 32.1 - - + +
29A GLY* 5.9 0.4 - - - -
31A ASP* 4.0 19.4 - - + +
32A PRO 2.8 12.4 + - - +
33A LEU* 3.5 12.6 - - - +
35A LEU* 1.3 78.3 - - - +
37A ALA* 1.3 55.9 + - - +
39A LYS* 3.4 6.2 + - + +
40A ASN* 3.0 32.7 + - + +
100A VAL* 3.5 24.9 - - + -
101A LEU* 3.9 27.6 - - + +
204A PRO* 3.6 25.6 - - + +
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Residues in contact with ALA 37 (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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8A MET* 4.1 15.4 - - + +
33A LEU 2.8 19.3 + - - +
34A TRP 3.8 4.0 - - - +
36A TYR* 1.3 70.5 - - - +
38A THR* 1.3 60.1 + - - +
40A ASN* 3.2 5.3 + - - +
41A LEU* 3.0 30.1 + - - +
97A VAL* 3.6 25.8 - - - +
99A ARG 4.8 1.3 - - - +
100A VAL* 3.9 23.2 - - + +
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Residues in contact with THR 38 (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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6A LEU* 4.7 0.8 - - + +
8A MET* 3.5 38.0 - - + +
34A TRP* 2.6 25.2 + - - -
35A LEU* 3.8 6.9 - - - -
37A ALA* 1.3 73.8 - - - +
39A LYS* 1.3 66.7 + - - +
41A LEU* 4.0 1.2 - - - +
42A SER* 3.0 27.5 + - - -
50A ILE* 4.1 7.2 - - + -
52A VAL* 3.8 17.2 - - + +
67A TYR* 3.8 31.9 - - + -
97A VAL* 4.3 1.0 - - - +
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Residues in contact with LYS 39 (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 ASP* 3.3 36.1 + - - +
35A LEU* 2.7 42.5 + - + +
36A TYR* 3.6 5.4 - - + +
38A THR* 1.3 74.2 - - - +
40A ASN* 1.3 61.1 + - - +
42A SER* 3.3 2.5 + - - -
43A SER* 3.1 23.9 + - - -
67A TYR* 3.8 16.8 + - - +
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Residues in contact with ASN 40 (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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36A TYR* 3.0 23.0 + - + +
37A ALA 3.2 7.9 + - - +
39A LYS* 1.3 75.9 - - - +
41A LEU* 1.3 65.4 + - - +
43A SER* 3.1 23.1 + - - -
44A PHE* 3.2 29.3 - - - -
100A VAL 3.6 21.3 + - - +
101A LEU* 5.2 3.4 - - - -
102A VAL* 2.8 31.2 + - - +
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Residues in contact with LEU 41 (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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6A LEU* 3.8 22.9 - - + -
8A MET* 3.5 28.3 - - + -
37A ALA 3.0 13.6 + - - +
38A THR 4.1 2.5 - - - +
40A ASN* 1.3 79.8 - - - +
42A SER* 1.3 58.6 + - - +
44A PHE* 3.1 39.6 + - + +
47A PHE* 3.6 12.5 - - + -
93A MET* 4.8 6.1 - - - -
95A SER* 3.6 25.8 - - - +
99A ARG 6.1 0.4 - - - +
102A VAL* 4.0 32.3 - - + -
107A PHE* 5.3 2.2 - - + -
148A PRO* 4.0 11.7 - - + -
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Residues in contact with SER 42 (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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6A LEU* 4.8 3.1 - - - +
38A THR* 3.0 21.0 + - - -
39A LYS* 3.7 4.3 - - - -
40A ASN 3.2 0.4 - - - -
41A LEU* 1.3 75.2 - - - +
43A SER* 1.3 63.1 + - - +
44A PHE 3.1 0.2 - - - -
45A TYR 3.3 15.6 + - - +
47A PHE* 4.3 9.8 - - - -
50A ILE* 3.4 28.6 - - - +
67A TYR* 4.3 13.1 + - - -
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Residues in contact with SER 43 (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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39A LYS 3.1 11.8 + - - -
40A ASN* 3.1 9.1 + - - -
41A LEU 3.2 0.4 - - - -
42A SER* 1.3 77.3 - - - +
44A PHE* 1.3 85.5 + - - +
45A TYR 3.4 1.5 + - - -
104A LYS* 5.2 1.0 + - - -
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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