Contacts of the strand formed by residues 22 - 30 (chain A) in PDB entry 1H10
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 TRP 22 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A HIS* 3.8 36.4 + + + +
14A LYS 3.8 0.2 - - - -
15A ARG* 3.7 40.3 - - + +
20A LYS 5.2 3.4 - - - -
21A THR* 1.3 74.1 - - - +
23A ARG* 1.3 62.2 + - - +
24A PRO* 4.2 3.1 - - - +
68A PRO* 3.9 27.0 - - + +
69A ARG* 3.8 31.1 - - + +
72A THR* 3.9 14.8 - - + -
87A THR* 3.7 22.2 - - + -
88A PHE 3.7 11.7 - - - -
89A HIS* 3.5 24.2 - - + -
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Residues in contact with ARG 23 (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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13A HIS* 3.3 3.8 - - - -
14A LYS 2.9 35.0 + - - +
15A ARG 5.5 0.2 - - - -
16A GLY* 3.8 7.8 - - - +
19A ILE* 2.8 37.5 + - - +
21A THR* 3.2 22.9 + - - +
22A TRP* 1.3 77.9 - - - +
24A PRO* 1.3 71.1 - - + +
25A ARG* 3.4 33.1 + - - +
1118A 4IP 2.8 60.3 + - - +
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Residues in contact with PRO 24 (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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11A TRP* 4.1 17.3 - - + -
12A LEU 3.5 7.4 - - - +
13A HIS* 3.6 21.1 - - + +
22A TRP 4.2 2.9 - - - +
23A ARG* 1.3 85.2 - - + +
25A ARG* 1.3 81.0 + - - +
39A LYS* 4.2 8.5 - - - +
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Residues in contact with ARG 25 (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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11A TRP* 3.4 8.4 - - - -
12A LEU* 2.9 39.2 + - + +
14A LYS* 3.9 15.7 - - + -
23A ARG* 3.5 36.6 - - - +
24A PRO* 1.3 99.9 + - - +
26A TYR* 1.3 61.3 + - - +
27A PHE* 3.6 22.4 - - + -
38A TYR 3.4 12.3 - - - +
39A LYS* 4.1 28.5 - - - +
52A LEU* 3.6 18.8 - - - +
53A ASN* 3.6 14.6 - - - +
1118A 4IP 2.9 37.6 + - - -
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Residues in contact with TYR 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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9A GLU* 2.6 40.8 + - + +
10A GLY* 3.6 23.4 + - - -
11A TRP* 3.6 37.1 - + + -
25A ARG* 1.3 71.7 - - - +
27A PHE* 1.3 71.6 + - - +
28A LEU* 5.0 5.8 - - + -
37A GLY* 3.2 1.7 - - - -
38A TYR* 2.9 45.8 + + + +
41A ARG* 3.3 62.8 + - + -
42A PRO* 4.1 12.1 - - + -
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Residues in contact with PHE 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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9A GLU* 3.1 5.5 - - - +
10A GLY 2.9 38.6 + - - +
12A LEU* 3.5 28.0 - - + -
14A LYS* 3.9 8.7 - - + -
25A ARG* 3.6 24.9 - - + -
26A TYR* 1.3 77.9 - - - +
28A LEU* 1.3 59.1 + - - +
35A PHE* 3.6 48.9 - + + -
36A ILE 3.2 17.3 - - - -
37A GLY* 3.5 22.0 - - - -
53A ASN* 3.9 15.0 - - + -
55A PHE* 4.1 11.9 - + - -
88A PHE* 3.8 19.7 - + - -
99A TRP* 3.9 4.4 - - + -
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Residues in contact with LEU 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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6A ILE* 3.8 35.7 - - + -
8A LYS 3.6 4.7 - - - -
9A GLU* 4.1 11.4 - - + +
26A TYR* 5.0 5.2 - - + -
27A PHE* 1.3 75.9 - - - +
29A LEU* 1.3 60.2 + - - +
30A LYS* 3.6 39.9 - - + +
34A THR 3.7 1.7 - - - +
35A PHE* 3.5 5.0 - - - -
36A ILE* 2.8 46.3 + - + +
38A TYR* 4.5 18.8 - - + +
42A PRO* 5.8 2.5 - - + -
48A ARG* 4.2 20.4 - - - +
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Residues in contact with LEU 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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6A ILE* 3.5 4.3 - - - -
7A VAL* 2.8 31.4 + - + -
8A LYS* 2.9 17.4 + - + +
28A LEU* 1.3 73.6 - - - +
30A LYS* 1.3 68.9 + - - +
34A THR 3.5 13.2 - - - +
35A PHE* 4.0 21.3 - - + -
57A VAL* 4.3 23.8 - - + -
99A TRP* 4.3 6.3 - - + -
102A ALA* 3.6 43.7 - - + +
103A ILE* 3.7 14.4 - - + +
106A VAL* 3.7 14.8 - - + -
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Residues in contact with LYS 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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3A ASP 4.3 1.3 - - - +
4A VAL* 3.2 33.2 - - + +
5A ALA 3.1 11.2 - - - +
6A ILE* 4.3 4.0 - - + -
7A VAL* 4.0 4.7 - - - -
28A LEU* 3.6 22.7 - - + +
29A LEU* 1.3 74.0 - - - +
31A ASN* 1.3 64.8 + - - +
32A ASP* 3.0 26.0 - - - +
33A GLY* 3.0 14.0 + - - -
34A THR* 3.0 29.6 + - - +
36A ILE* 4.0 24.5 - - - +
106A VAL* 3.5 11.1 - - - +
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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