Contacts of the strand formed by residues 1061 - 1064 (chain H) in PDB entry 4A63
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 VAL1061 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1057H MET 4.0 1.4 + - - +
1058H ASN* 3.2 27.0 + - + +
1059H LYS* 3.9 12.3 - - + +
1060H GLY* 1.3 75.4 - - - +
1062H ILE* 1.3 66.5 + - - +
1063H TYR* 4.2 14.8 - - + +
1083H CYS* 3.6 29.6 - - - -
1084H MET 3.5 4.9 - - - +
1085H THR* 4.1 13.7 - - - +
1116H LEU* 4.1 17.7 - - - +
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Residues in contact with ILE1062 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054H MET* 3.9 23.6 - - + -
1055H GLY* 3.8 28.3 - - - +
1061H VAL* 1.3 78.2 - - - +
1063H TYR* 1.3 73.4 + - - +
1083H CYS* 3.7 2.9 - - - -
1084H MET* 3.0 56.8 + - + +
1086H ILE* 3.6 23.1 - - + -
1098H TRP* 4.6 0.7 - - + -
1114H LEU* 3.6 36.3 - - + -
1115H GLY 3.4 12.3 - - - +
1116H LEU* 4.5 2.0 - - + -
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Residues in contact with TYR1063 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061H VAL* 4.2 16.4 - - + +
1062H ILE* 1.3 80.5 - - - +
1064H ALA* 1.3 64.4 + - - +
1065H LEU* 4.1 0.8 - - + +
1081H GLY 3.7 18.2 - - - +
1082H ASP 3.2 5.6 - - - +
1083H CYS* 3.6 34.1 - - + -
1114H LEU* 3.5 4.0 - - - -
1115H GLY* 2.8 36.5 + - - +
1116H LEU 3.4 23.8 - - - -
1117H TYR* 3.6 15.8 - + - +
1118H PRO* 3.7 44.6 - - + -
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Residues in contact with ALA1064 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063H TYR* 1.3 72.1 - - - +
1065H LEU* 1.3 60.5 + - - +
1066H TRP 3.4 10.1 - - - +
1078H MET* 3.8 18.6 - - + -
1079H LYS 3.5 21.1 - - - +
1080H GLU* 4.1 1.4 - - - +
1081H GLY* 2.8 28.3 + - - -
1082H ASP* 2.8 10.7 + - + +
1084H MET* 3.7 20.5 - - + +
1113H LEU 3.9 4.9 - - - -
1114H LEU* 4.2 2.5 - - - -
1118H PRO* 5.5 0.5 - - - +
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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