Contacts of the helix formed by residues 32 - 45 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208L CYS* 4.9 3.4 - - - -
207M SER* 3.6 33.3 - - - +
30N GLN 4.5 5.4 - - - +
31N TYR* 1.3 74.6 - - - +
33N ALA* 1.3 67.3 + - - +
34N GLU* 3.8 6.7 + - - +
35N GLU* 3.2 26.0 + - - +
36N TYR* 2.8 20.3 + - - +
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Residues in contact with ALA 33 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205L TYR* 3.5 31.2 - - + +
208L CYS* 3.2 45.0 + - + +
209L ARG* 4.6 10.1 - - + +
32N THR* 1.3 71.8 - - - +
34N GLU* 1.3 57.5 + - - +
36N TYR* 3.6 1.6 - - - +
37N GLN* 2.8 33.3 + - - +
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Residues in contact with GLU 34 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205L TYR* 4.8 7.8 + - - +
199M SER 5.3 0.5 - - - +
202M GLU* 4.7 1.2 - - - +
203M ALA* 3.7 23.0 + - + +
206M ASN* 3.7 36.0 + - - +
32N THR* 3.1 7.0 + - - +
33N ALA* 1.3 81.4 - - - +
35N GLU* 1.3 63.7 + - - +
37N GLN* 3.4 6.2 + - - +
38N ALA* 3.0 23.6 + - - +
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Residues in contact with GLU 35 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81M TYR* 4.5 0.4 - - - -
200M VAL* 4.8 1.8 - - + +
203M ALA* 3.6 17.6 - - + +
204M ARG* 2.7 51.9 + - + +
207M SER* 4.0 11.1 + - - -
31N TYR* 3.5 26.9 - - + -
32N THR* 3.2 18.7 + - - +
34N GLU* 1.3 75.2 - - - +
36N TYR* 1.3 66.7 + - - +
38N ALA* 3.2 0.9 + - - +
39N ILE* 3.0 36.7 + - + +
79N PHE 4.6 0.9 - - - +
116N LYS* 3.3 18.1 + - - -
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Residues in contact with TYR 36 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L GLU* 2.7 28.6 + - - -
204L ARG* 2.7 41.9 + - + -
205L TYR* 4.6 12.3 - + - -
208L CYS* 4.8 14.1 - - - -
80M GLY* 4.3 1.8 - - - -
81M TYR* 3.5 25.6 - + - -
82M ASN* 3.6 28.0 - - - +
31N TYR* 4.1 12.4 - - + +
32N THR 2.8 17.8 + - - +
33N ALA* 3.6 7.0 - - - +
35N GLU* 1.3 77.0 - - - +
37N GLN* 1.3 64.0 + - + +
40N GLN* 2.8 56.3 + - + +
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Residues in contact with GLN 37 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L GLU* 4.4 10.3 - - - +
205L TYR* 3.1 43.1 + - + -
33N ALA 2.8 17.5 + - - +
34N GLU* 3.8 6.1 + - - +
36N TYR* 1.3 86.0 - - + +
38N ALA* 1.3 64.6 + - - +
40N GLN* 3.4 3.1 + - - +
41N LYS* 2.9 59.4 + - - +
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Residues in contact with ALA 38 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199M SER* 4.0 17.3 + - - +
200M VAL* 3.6 30.9 - - + +
203M ALA* 4.2 3.8 - - + -
34N GLU 3.0 17.2 + - - +
35N GLU 3.7 3.4 - - - +
37N GLN* 1.3 80.8 - - - +
39N ILE* 1.3 58.0 - - - +
41N LYS* 3.4 6.9 + - - +
42N ALA* 2.8 29.3 + - - +
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Residues in contact with ILE 39 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M TYR* 3.4 38.6 - - + +
200M VAL* 3.8 23.3 - - + -
204M ARG* 4.2 1.1 - - - +
31N TYR* 3.9 6.7 - - + -
35N GLU* 3.0 42.0 + - + +
38N ALA* 1.3 73.3 - - - +
40N GLN* 1.4 65.0 + - - +
42N ALA* 4.2 1.8 - - - -
43N LEU* 2.8 43.0 + - + +
78N MET* 3.8 18.2 - - - +
79N PHE* 4.1 16.2 - - + -
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Residues in contact with GLN 40 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L GLU* 4.4 10.3 - - - +
204L ARG* 4.6 1.6 + - - -
76M ASN* 3.0 26.9 + - - +
77M GLU* 3.9 16.5 + - - +
80M GLY* 3.4 5.7 - - - -
81M TYR* 3.8 25.5 - - + +
36N TYR* 2.8 53.9 + - + +
37N GLN* 3.7 5.8 - - - +
39N ILE* 1.4 77.1 - - - +
41N LYS* 1.3 64.1 + - - +
43N LEU* 3.6 9.9 + - - +
44N ARG* 3.6 25.7 + - - +
158N PHE 5.8 0.2 + - - -
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Residues in contact with LYS 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201L GLU* 5.4 3.1 - - - +
37N GLN* 2.9 50.4 + - - +
38N ALA* 3.6 8.7 - - - +
39N ILE 3.2 0.2 - - - -
40N GLN* 1.3 79.8 - - + +
42N ALA* 1.3 65.5 + - - +
44N ARG* 3.1 46.4 + - - +
45N GLN* 4.0 5.6 + - - +
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Residues in contact with ALA 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197M GLU* 3.7 22.0 - - - +
199M SER* 5.5 1.1 - - - +
200M VAL* 4.0 6.3 - - + -
38N ALA 2.8 21.5 + - - +
39N ILE 3.7 0.7 - - - +
41N LYS* 1.3 73.8 - - - +
43N LEU* 1.3 62.7 + - - +
44N ARG 3.2 0.9 + - - -
45N GLN* 3.3 27.3 + - - +
78N MET* 3.6 27.1 - - + +
161N ALA* 3.4 10.9 - - - +
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Residues in contact with LEU 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81M TYR* 3.3 29.8 - - + -
39N ILE* 2.8 35.6 + - + +
40N GLN* 3.9 7.9 - - - +
41N LYS 3.2 0.2 - - - -
42N ALA* 1.3 77.5 - - - +
44N ARG* 1.3 56.9 + - + +
45N GLN 3.3 0.2 - - - -
78N MET* 3.8 15.7 - - + -
79N PHE* 4.5 2.5 - - + -
158N PHE* 3.3 37.2 - - + +
159N GLY* 3.9 2.2 - - - -
160N ASN 3.1 9.7 + - - -
161N ALA* 2.9 28.0 + - + -
162N LEU* 3.6 31.2 - - + -
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Residues in contact with ARG 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L LEU* 3.7 31.3 - - - +
201L GLU* 4.9 12.5 + - - +
77M GLU* 2.5 53.6 + - - +
40N GLN* 3.6 27.8 + - - +
41N LYS* 3.1 41.7 + - - +
43N LEU* 1.3 76.7 - - - +
45N GLN* 1.3 62.0 + - + +
46N ARG* 3.5 3.5 + - - +
160N ASN* 2.8 27.7 + - - +
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Residues in contact with GLN 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190M LYS 4.9 8.7 - - - +
192M LYS* 2.9 42.3 - - + +
197M GLU* 3.0 23.4 + - - +
41N LYS 4.4 4.0 - - - +
42N ALA* 3.4 20.9 + - - +
43N LEU 3.3 1.0 - - - -
44N ARG* 1.3 77.6 - - - +
46N ARG* 1.3 66.6 + - - +
160N ASN* 3.1 2.6 - - - +
161N ALA* 2.9 29.8 + - + -
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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