Contacts of the helix formed by residues 32 - 45 (chain P) in PDB entry 1H2I
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 THR 32 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208N CYS 5.3 1.6 - - - -
203O ALA 4.8 1.9 + - - -
206O ASN 5.4 1.1 - - - +
207O SER* 3.8 33.3 - - - +
30P GLN 4.4 5.2 - - - +
31P TYR* 1.3 75.5 - - - +
33P ALA* 1.3 65.6 + - - +
34P GLU* 3.6 7.6 + - - +
35P GLU* 3.2 24.6 + - - +
36P TYR* 2.9 21.4 + - - +
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Residues in contact with ALA 33 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205N TYR* 3.8 28.6 - - + +
208N CYS* 3.6 40.5 + - + +
209N ARG* 4.4 9.6 - - + +
31P TYR 3.9 1.4 + - - -
32P THR* 1.3 72.0 - - - +
34P GLU* 1.3 64.5 + - - +
36P TYR* 3.7 1.5 - - - +
37P GLN* 2.9 27.4 + - - +
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Residues in contact with GLU 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205N TYR* 4.9 6.9 + - - +
199O SER 5.1 0.5 - - - +
202O GLU* 3.1 28.1 - - - +
203O ALA* 3.7 19.7 - - + +
206O ASN* 3.3 23.0 + - - +
32P THR* 3.1 8.1 + - - +
33P ALA* 1.3 80.6 - - - +
35P GLU* 1.3 63.0 - - - +
37P GLN* 3.7 5.9 + - - +
38P ALA* 3.0 22.7 + - - +
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Residues in contact with GLU 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200O VAL* 4.8 2.2 - - + +
203O ALA* 3.5 16.5 - - + +
204O ARG* 2.8 48.4 + - - +
207O SER* 3.6 17.5 + - - -
31P TYR* 3.6 25.4 - - + -
32P THR* 3.2 16.1 + - - +
34P GLU* 1.3 74.9 - - - +
36P TYR* 1.3 67.7 + - - +
38P ALA* 3.1 2.0 + - - +
39P ILE* 2.9 36.7 + - + +
79P PHE 4.5 0.5 - - - +
116P LYS* 3.3 21.6 + - - -
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Residues in contact with TYR 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201N GLU* 3.2 19.3 + - - -
204N ARG* 2.8 44.6 + - - -
205N TYR* 5.0 6.7 - + - -
208N CYS* 4.1 21.8 - - - -
80O GLY* 4.0 1.7 - - - -
81O TYR* 3.4 25.4 - + - -
82O ASN* 3.6 28.5 - - - -
31P TYR* 4.1 11.6 - - + +
32P THR 2.9 18.3 + - - +
33P ALA 3.7 4.7 - - - +
35P GLU* 1.3 77.7 - - - +
37P GLN* 1.3 76.8 + - + +
40P GLN* 2.8 63.0 + - + +
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Residues in contact with GLN 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201N GLU* 5.4 4.3 - - - +
205N TYR* 3.0 41.2 + - + -
33P ALA 2.9 18.0 + - - +
34P GLU* 3.7 5.2 + - - +
36P TYR* 1.3 88.7 - - + +
38P ALA* 1.3 64.4 + - - +
40P GLN* 3.4 3.2 + - + +
41P LYS* 2.9 60.7 + - - +
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Residues in contact with ALA 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199O SER* 4.3 13.5 + - - +
200O VAL* 3.7 35.5 - - + +
203O ALA* 4.5 3.4 - - + -
34P GLU 3.0 17.0 + - - +
35P GLU 3.1 4.5 + - - +
37P GLN* 1.3 79.6 - - - +
39P ILE* 1.3 58.0 + - - +
41P LYS* 3.7 7.1 - - - +
42P ALA* 2.9 28.8 + - - +
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Residues in contact with ILE 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O TYR* 3.4 36.3 - - + +
200O VAL* 3.7 22.4 - - + -
204O ARG* 4.1 1.3 - - - +
31P TYR* 3.9 7.6 - - + -
35P GLU* 2.9 43.0 + - + +
38P ALA* 1.3 74.6 - - - +
40P GLN* 1.3 65.6 + - - +
42P ALA* 4.3 1.8 - - - +
43P LEU* 2.9 46.5 + - + +
78P MET* 3.7 21.3 - - - +
79P PHE* 4.2 14.4 - - + -
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Residues in contact with GLN 40 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201N GLU* 3.7 14.6 - - - +
204N ARG* 4.6 0.2 + - - -
76O ASN* 3.1 26.3 + - - +
77O GLU* 4.1 11.5 + - - +
80O GLY* 3.5 5.5 - - - -
81O TYR* 3.7 28.1 - - + +
36P TYR* 2.8 56.0 + - + +
37P GLN* 3.7 7.0 - - + +
39P ILE* 1.3 73.9 - - - +
41P LYS* 1.3 64.0 + - + +
43P LEU* 3.6 8.9 + - - +
44P ARG* 3.5 30.3 + - - +
158P PHE 5.7 0.2 + - - -
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Residues in contact with LYS 41 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37P GLN* 2.9 50.3 + - - +
38P ALA* 3.7 8.5 - - - +
39P ILE 3.1 0.4 - - - -
40P GLN* 1.3 78.4 - - + +
42P ALA* 1.3 67.2 + - - +
44P ARG* 3.1 44.9 + - - +
45P GLN* 4.0 4.7 + - - +
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Residues in contact with ALA 42 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197O GLU* 3.6 23.3 - - - +
200O VAL* 4.0 5.2 - - + -
38P ALA 2.9 18.4 + - - +
39P ILE 3.2 1.3 + - - +
41P LYS* 1.3 74.8 - - - +
43P LEU* 1.3 63.6 + - - +
44P ARG 3.2 0.9 + - - -
45P GLN* 3.2 31.3 + - - +
78P MET* 3.6 26.9 - - + +
161P ALA* 3.4 7.6 - - - +
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Residues in contact with LEU 43 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81O TYR* 3.4 29.4 - - + -
39P ILE* 2.9 35.9 + - + +
40P GLN* 4.0 7.6 - - - +
41P LYS 3.1 0.4 + - - -
42P ALA* 1.3 75.0 - - - +
44P ARG* 1.3 57.3 + - - +
78P MET* 3.7 17.3 - - + -
79P PHE* 4.5 4.7 - - + -
158P PHE* 3.4 33.0 - - + +
159P GLY* 4.5 0.9 - - - -
160P ASN 3.1 10.4 + - - -
161P ALA* 2.8 29.4 + - + -
162P LEU* 3.5 33.9 - - + +
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Residues in contact with ARG 44 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196N LEU* 3.4 22.0 - - - +
201N GLU* 4.6 15.8 + - - +
77O GLU* 2.5 53.7 + - - +
40P GLN* 3.5 29.2 + - - +
41P LYS* 3.1 41.6 + - - +
43P LEU* 1.3 76.5 - - - +
45P GLN* 1.3 60.7 + - + +
46P ARG* 3.5 3.5 + - - +
160P ASN* 2.8 27.8 + - - +
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Residues in contact with GLN 45 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190O LYS 5.1 6.7 - - - +
192O LYS* 2.9 52.4 - - + +
197O GLU* 3.5 13.8 + - - +
41P LYS 4.4 3.5 - - - +
42P ALA* 3.2 24.6 + - - +
44P ARG* 1.3 76.5 - - - +
46P ARG* 1.3 67.0 + - - +
160P ASN* 3.1 1.9 - - - +
161P ALA* 3.0 28.0 + - + -
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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