Contacts of the strand formed by residues 6 - 13 (chain A) in PDB entry 1H5Y
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 ARG 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5A LEU* 1.3 75.3 - - - +
7A ILE* 1.3 61.3 - - - +
8A ILE* 4.0 13.4 - - + +
48A ASP* 3.4 21.1 - - + +
49A GLU* 2.8 33.5 + - - -
102A LYS* 3.5 7.1 - - - +
170A GLU* 2.6 32.1 + - - -
200A PRO* 3.6 12.3 - - - +
202A ILE* 4.6 0.6 - - - +
222A ASP* 2.8 39.8 + - - +
223A ALA* 3.2 22.6 - - + +
224A VAL* 2.9 29.6 + - - +
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Residues in contact with ILE 7 (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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5A LEU* 4.0 11.2 - - + +
6A ARG* 1.3 76.6 - - - +
8A ILE* 1.3 59.5 + - - +
9A PRO* 4.2 0.2 - - - -
47A ALA* 3.8 2.6 - - - -
48A ASP* 2.8 46.4 + - - +
224A VAL* 3.4 27.1 - - + -
230A PHE* 3.9 29.4 - - + -
237A ILE* 4.1 21.3 - - + -
240A VAL* 4.3 8.3 - - + -
241A LYS* 3.9 23.6 - - + -
244A LEU* 3.7 26.5 - - + -
251A VAL* 4.7 0.7 - - + -
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Residues in contact with ILE 8 (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 ARG* 4.2 9.6 - - + +
7A ILE* 1.3 84.7 - - - +
9A PRO* 1.3 69.2 - - - +
49A GLU* 3.7 47.8 - - + +
51A ALA* 3.9 12.3 - - + +
81A LEU* 5.1 3.6 - - + -
202A ILE* 4.2 20.4 - - + -
223A ALA* 4.0 20.0 - - + -
224A VAL 2.9 14.7 + - - +
225A LEU* 3.1 42.2 - - + +
226A ALA 3.2 3.1 + - - -
230A PHE* 4.7 3.6 - - - -
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Residues in contact with PRO 9 (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 0.7 - - - +
8A ILE* 1.3 87.6 - - - +
10A CYS* 1.3 58.3 + - - +
11A LEU* 4.1 1.5 + - + -
42A TYR* 3.6 38.1 - - + -
47A ALA* 3.6 13.0 - - + -
49A GLU 3.2 18.8 - - - +
50A ILE* 4.0 6.1 - - + +
51A ALA 3.1 23.9 + - - +
225A LEU* 4.2 0.7 - - - -
226A ALA 3.4 7.4 - - - +
230A PHE* 4.0 13.0 - - + -
231A HIS* 4.9 0.2 - - + -
237A ILE* 3.5 27.6 - - + -
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Residues in contact with CYS 10 (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 PRO* 1.3 74.0 - - - +
11A LEU* 1.3 65.5 + - - +
12A ASP* 3.6 16.9 + - - -
51A ALA* 3.7 6.3 - - - -
53A LEU* 3.5 37.0 - - - -
225A LEU* 3.7 29.6 - - + -
226A ALA* 2.9 16.3 + - - +
227A ALA* 3.6 10.1 - - + +
231A HIS* 2.8 23.8 + - - -
302A PO4 6.1 0.2 - - - +
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Residues in contact with LEU 11 (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 PRO* 5.1 0.4 - - + -
10A CYS* 1.3 73.0 - - - +
12A ASP* 1.3 62.9 + - - +
13A ILE* 3.5 15.0 + - + +
19A VAL* 4.0 11.0 - - + -
35A PRO* 3.5 36.1 - - + +
38A MET* 4.2 8.5 - - + -
39A ALA* 4.2 9.0 - - + +
42A TYR* 3.9 20.0 - - + -
50A ILE* 4.1 21.1 - - + -
51A ALA 2.8 18.3 + - - +
52A ILE* 3.3 10.6 - - + -
53A LEU 2.9 24.9 + - - -
72A VAL* 5.0 1.6 - - + -
231A HIS* 3.8 23.1 - - + +
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Residues in contact with ASP 12 (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 CYS* 3.6 19.3 + - - -
11A LEU* 1.3 71.2 - - - +
13A ILE* 1.3 60.7 + - - +
19A VAL* 3.3 7.0 - - - +
20A VAL* 2.9 44.1 + - + +
22A LYS* 3.8 27.2 + - + +
53A LEU* 3.6 16.7 - - - +
55A ILE* 3.9 21.5 - - + +
227A ALA* 3.6 24.9 - - - +
302A PO4 5.5 0.3 + - - -
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Residues in contact with ILE 13 (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 LEU* 3.7 12.3 - - + +
12A ASP* 1.3 75.3 - - - +
14A ASP* 1.3 59.7 + - - +
15A GLY* 3.4 24.4 + - - +
18A LYS* 3.6 6.1 - - - +
19A VAL* 3.6 30.7 - - + -
35A PRO* 4.0 18.6 - - + -
52A ILE* 3.5 26.7 - - + -
53A LEU 2.8 13.9 + - - +
54A ASP* 3.8 5.2 - - - +
55A ILE* 3.2 23.8 + - - +
56A THR* 3.9 0.3 - - - +
65A PHE* 3.9 23.8 - - + -
68A SER* 5.1 9.2 - - - +
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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