Contacts of the strand formed by residues 62 - 66 (chain O) 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 LYS 62 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54O SER* 3.5 33.0 - - - +
55O ARG 3.6 0.2 - - - -
56O MET* 3.4 25.1 - - + +
61O GLN* 1.3 78.9 + - - +
63O VAL* 1.3 65.3 + - - +
64O CYS* 4.2 17.0 - - - -
176O ASN* 3.7 30.3 + - - +
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Residues in contact with VAL 63 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54O SER* 3.1 5.5 - - - -
55O ARG* 3.0 61.3 + - + +
57O ALA* 3.5 31.6 - - + +
61O GLN* 3.6 2.7 - - + +
62O LYS* 1.3 80.6 - - - +
64O CYS* 1.3 74.2 + - - +
65O TYR* 3.8 3.2 - - + -
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Residues in contact with CYS 64 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O ILE* 3.8 21.5 - - + -
53O SER 3.4 3.6 - - - -
54O SER* 4.4 3.1 - - - -
62O LYS* 4.3 29.2 - - - -
63O VAL* 1.3 85.0 - - - +
65O TYR* 1.3 65.6 + - - +
166O ILE* 3.5 18.5 - - + +
172O LEU* 3.9 28.0 - - + +
175O LEU* 5.8 1.8 - - - -
176O ASN* 5.9 2.9 - - - -
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Residues in contact with TYR 65 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O ILE* 3.9 2.7 - - - +
53O SER* 3.0 57.8 + - - +
54O SER* 3.8 29.3 + - - -
55O ARG* 3.2 41.4 - - + +
63O VAL* 3.8 9.4 - - + -
64O CYS* 1.3 75.9 - - - +
66O ILE* 1.3 75.8 + - - +
67O GLU* 3.7 24.0 + - + -
152O LYS* 4.2 13.7 - - - +
156O ARG* 6.2 2.9 - - - +
166O ILE* 3.6 10.7 - - - +
169P LYS* 5.4 3.6 + - - -
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Residues in contact with ILE 66 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47O LEU* 4.1 17.9 - - + -
51O TYR* 3.7 20.2 - - + +
52O ILE* 4.1 13.0 - - + -
65O TYR* 1.3 80.4 - - - +
67O GLU* 1.3 68.9 + - - +
70O ARG* 3.9 13.5 - - + -
71O VAL* 3.7 26.7 - - + +
74O LEU* 5.1 2.2 - - + -
152O LYS* 3.0 29.8 + - + +
156O ARG* 5.0 8.1 - - - +
162O LEU 5.0 0.9 - - - +
163O GLY* 3.9 28.5 - - - +
165O CYS* 5.9 0.4 - - - -
166O ILE* 3.8 20.4 - - + +
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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