Contacts of the strand formed by residues 6 - 13 (chain A) in PDB entry 1HDZ
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 VAL 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A THR* 5.5 1.4 - - - +
5A LYS* 1.3 86.3 + - - +
7A ILE* 1.3 75.7 + - - +
8A LYS* 5.8 0.9 - - + -
27A GLU* 3.7 25.1 - - + -
28A VAL 3.6 6.1 - - - +
29A ALA* 4.0 10.3 - - + -
30A PRO* 3.9 17.3 - - + -
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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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2A THR* 3.8 29.6 - - + -
6A VAL* 1.3 79.9 - - - +
8A LYS* 1.3 74.0 + - - +
9A CYS* 4.2 4.9 - - - -
26A VAL 3.6 0.2 - - - +
27A GLU* 3.1 5.2 - - - -
28A VAL* 2.9 37.3 + - + +
37A ARG* 3.3 19.5 - - - +
74A GLU* 3.4 26.0 - - - +
149A TYR* 3.6 48.9 - - + -
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Residues in contact with LYS 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 VAL* 4.4 1.1 + - + -
7A ILE* 1.3 79.0 - - - +
9A CYS* 1.3 63.8 + - - +
25A ASP* 3.3 49.6 + - + +
26A VAL 3.1 12.1 - - - +
27A GLU* 2.9 39.2 + - + -
133A ARG 5.6 1.4 - - - +
149A TYR* 5.8 0.2 - - - -
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Residues in contact with CYS 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* 4.2 1.3 - - - -
8A LYS* 1.3 75.1 - - - +
10A LYS* 1.3 81.8 + - - +
25A ASP* 3.1 5.4 - - - -
26A VAL* 2.8 35.7 + - - +
28A VAL* 3.5 32.1 - - - -
147A SER* 4.0 2.9 - - - -
148A GLN* 3.4 19.7 - - + +
149A TYR* 4.0 31.4 - - + -
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A CYS* 1.3 81.6 - - - +
11A ALA* 1.3 62.1 + - - +
23A ILE* 3.7 25.1 - - + +
24A GLU* 3.0 15.5 - - - +
25A ASP* 2.8 37.0 + - - +
148A GLN* 2.9 44.8 + - - +
352A PHE* 3.9 12.1 - - + -
353A GLU* 5.0 7.4 - - - +
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Residues in contact with ALA 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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10A LYS* 1.3 77.2 - - - +
12A ALA* 1.3 60.6 + - - +
13A VAL* 3.6 2.7 + - + +
22A SER 3.2 1.6 - - - +
23A ILE* 3.3 1.7 - - - -
24A GLU* 2.9 28.1 + - - +
26A VAL* 3.8 15.7 - - + -
64A ILE* 3.7 22.4 - - + -
146A PHE 3.5 6.3 - - - +
147A SER* 3.5 22.9 - - - +
352A PHE* 3.5 8.3 - - - -
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Residues in contact with ALA 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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11A ALA* 1.3 69.8 - - - +
13A VAL* 1.3 61.6 + - - +
21A PHE* 3.7 33.1 - - + -
22A SER 3.4 6.5 - - - +
23A ILE* 4.3 3.6 - - + +
63A VAL 4.1 0.5 - - - +
64A ILE* 3.7 23.0 - - - +
65A LEU 4.5 2.1 + - - -
146A PHE* 3.0 13.8 + - + +
352A PHE* 3.6 7.0 - - + -
355A ILE* 4.0 28.0 - - + -
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Residues in contact with VAL 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 ALA 4.2 4.9 - - - +
12A ALA* 1.3 77.8 - - - +
14A LEU* 1.3 67.7 + - - +
15A TRP* 3.5 40.1 + - + +
20A PRO 4.3 0.7 - - - +
21A PHE* 3.5 6.2 - - - -
22A SER* 2.9 36.5 + - - +
24A GLU* 4.4 7.6 - - + -
26A VAL* 4.1 18.4 - - + -
62A PRO* 4.2 7.9 - - + -
63A VAL 3.7 6.5 - - - +
64A ILE* 3.8 21.5 - - + -
132A CYS* 4.6 4.0 - - + -
137A ILE* 4.2 10.8 - - + -
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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