Contacts of the helix formed by residues 27 - 40 (chain A) in PDB entry 2W3A
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 27 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A LEU* 5.9 1.6 - - - +
24A TRP* 4.1 14.2 - - + +
25A PRO 3.3 15.5 + - - +
26A PRO* 1.3 75.0 - - - +
28A ARG* 1.3 60.0 - - - +
29A ASN 3.5 2.0 - - - -
30A GLU* 3.2 12.9 + - + +
31A PHE* 3.0 28.3 + - - +
138A ILE* 3.9 27.8 - - + -
172A GLU* 3.7 42.2 - - + +
173A LYS* 4.5 5.4 - - + -
175A ILE* 4.1 21.8 - - + -
177A TYR* 4.1 17.5 - - + -
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Residues in contact with ARG 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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26A PRO* 3.8 32.2 + - - +
27A LEU* 1.3 73.3 - - - +
29A ASN* 1.3 62.2 + - - +
31A PHE* 3.4 17.9 + - - +
32A ARG* 3.0 32.7 + - + +
172A GLU* 3.4 8.9 + - - +
173A LYS* 5.2 2.2 - - - +
1189A SO4 2.9 43.1 + - - +
1190A TOP 6.3 1.4 - - - -
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Residues in contact with ASN 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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28A ARG* 1.3 72.0 - - - +
30A GLU* 1.3 59.2 + - - +
32A ARG* 3.3 21.6 + - + +
33A TYR* 2.9 27.7 + - - +
172A GLU* 2.9 31.2 + - - +
177A TYR* 4.1 6.1 - - - +
179A PHE* 5.1 1.3 - - - -
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Residues in contact with GLU 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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9A ALA* 4.1 4.9 - - - +
24A TRP* 5.6 3.2 + - - -
27A LEU* 3.2 29.5 + - + +
29A ASN* 1.3 75.6 - - - +
31A PHE* 1.3 62.3 + - - +
33A TYR* 3.2 8.8 + - - +
34A PHE* 3.1 18.0 + - - +
136A THR* 2.8 43.2 + - + -
138A ILE* 5.1 1.6 - - + -
172A GLU* 3.1 8.8 + - - +
177A TYR* 3.6 19.7 + - + +
179A PHE* 4.1 5.4 - - + -
1190A TOP 2.7 40.1 + - - -
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Residues in contact with PHE 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 LEU 3.0 13.3 + - - +
28A ARG* 3.7 21.8 - - - +
30A GLU* 1.3 77.4 + - - +
32A ARG* 1.3 65.6 + - + +
34A PHE* 3.2 12.1 + + + +
35A GLN* 2.9 70.7 + - + +
64A ASN* 4.9 14.8 - - - -
67A LEU* 5.9 1.3 - - + -
1190A TOP 3.0 59.0 - + + -
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Residues in contact with ARG 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 ARG* 3.0 20.9 + - + +
29A ASN* 3.3 24.9 + - - +
31A PHE* 1.3 79.5 - - + +
33A TYR* 1.3 56.9 + - - +
35A GLN* 3.4 7.9 + - - +
36A ARG* 2.9 30.1 + - - +
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Residues in contact with TYR 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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7A ILE* 4.2 15.3 - - + -
29A ASN 2.9 13.5 + - - +
30A GLU* 3.3 15.9 - - - +
32A ARG* 1.3 72.7 - - - +
34A PHE* 1.3 66.3 + - - +
36A ARG* 3.2 32.9 + - - +
37A MET* 2.9 50.7 + - + +
134A PHE* 3.6 28.1 - - + +
135A VAL 6.3 0.2 - - - -
136A THR* 4.3 5.4 - - - -
165A VAL* 3.7 25.7 - - + +
179A PHE* 3.4 52.7 - + + +
180A GLU 5.0 1.2 + - - -
181A VAL* 4.9 0.9 - - - +
1190A TOP 4.9 0.4 - - - -
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Residues in contact with PHE 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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7A ILE* 3.8 22.2 - - + -
30A GLU 3.1 12.6 + - - +
31A PHE* 3.4 20.0 - + + +
33A TYR* 1.3 75.5 - - - +
35A GLN* 1.3 79.1 + - - +
37A MET 4.0 0.2 - - - -
38A THR* 2.8 40.4 + - + +
67A LEU* 4.1 11.9 - - + -
70A ARG* 4.0 9.0 - - - -
115A VAL* 3.7 31.6 - - + -
1190A TOP 3.5 77.2 - + + +
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Residues in contact with GLN 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 PHE* 2.9 57.9 + - + +
32A ARG* 3.7 7.6 - - - +
33A TYR 3.2 0.2 - - - -
34A PHE* 1.3 86.0 - - - +
36A ARG* 1.3 58.0 + - - +
38A THR* 3.9 2.7 - - - -
39A THR* 2.6 37.2 + - - +
64A ASN* 6.0 0.8 - - - +
67A LEU* 4.2 6.9 - - - +
70A ARG* 2.8 39.9 + - - +
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Residues in contact with ARG 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 ARG 2.9 17.9 + - - +
33A TYR* 3.2 30.2 + - - +
35A GLN* 1.3 76.4 - - - +
37A MET* 1.3 79.2 + - - +
39A THR* 5.0 0.7 - - - -
40A THR* 2.7 44.2 + - + +
164A GLY* 3.0 33.3 + - - -
165A VAL* 5.0 0.6 - - - +
166A LEU* 5.6 0.8 - - - +
1187A GOL 3.5 27.2 + - - -
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Residues in contact with MET 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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7A ILE* 4.0 11.7 - - + -
33A TYR* 2.9 49.6 + - + +
36A ARG* 1.3 103.0 - - - +
38A THR* 1.3 63.3 + - - +
40A THR* 4.1 6.1 + - - +
48A ASN* 4.2 2.3 + - - -
111A MET* 4.7 1.4 - - - +
113A TRP* 3.2 40.8 + - + -
134A PHE* 3.5 34.5 - - + -
162A TYR* 5.9 1.8 - - + -
163A PRO 6.1 0.2 - - - +
164A GLY 4.9 0.4 - - - +
165A VAL* 4.8 6.7 - - + -
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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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7A ILE* 3.9 29.2 - - + -
34A PHE* 2.8 35.6 + - + +
35A GLN 3.7 0.2 + - - -
37A MET* 1.3 77.1 - - - +
39A THR* 1.3 58.1 + - - +
48A ASN* 3.0 27.0 + - - +
50A VAL* 4.2 8.0 - - - +
70A ARG* 2.9 38.5 + - - +
113A TRP* 3.9 25.1 - - + +
115A VAL* 4.2 3.1 - - + -
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Residues in contact with THR 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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35A GLN* 2.6 24.0 + - - +
36A ARG* 4.5 0.7 - - - -
38A THR* 1.3 78.4 - - - +
40A THR* 1.3 65.3 + - - +
41A SER* 3.3 4.5 + - - -
48A ASN* 3.7 7.2 + - - +
68A LYS 4.2 11.0 - - - +
69A GLY* 4.1 23.6 - - - +
70A ARG* 3.1 28.0 + - - +
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Residues in contact with THR 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 ARG* 2.7 37.6 + - + +
37A MET* 4.1 3.1 + - - +
38A THR 3.7 0.6 - - - -
39A THR* 1.3 75.5 - - - +
41A SER* 1.3 66.0 + - - +
42A SER* 4.9 2.9 - - - +
48A ASN* 3.0 14.6 + - - -
111A MET* 4.1 10.7 - - - +
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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