Contacts of the strand formed by residues 1061 - 1064 (chain D) in PDB entry 6GHM
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1055D GLY 5.3 0.2 + - - -
1057D MET 3.8 1.5 + - - +
1058D ASN* 3.1 20.2 + - - +
1059D LYS* 3.8 14.4 - - + +
1060D GLY* 1.3 77.3 - - - +
1062D ILE* 1.3 68.6 + - - +
1063D TYR* 3.9 3.6 - - + +
1083D CYS* 3.5 30.1 - - - -
1084D MET 3.4 5.8 - - - +
1085D THR* 4.4 11.7 - - - +
1116D LEU* 4.3 2.3 - - - +
1201D EDO 2.6 45.3 + - - -
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Residues in contact with ILE1062 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054D MET* 3.4 40.4 - - + -
1055D GLY* 3.9 13.5 - - - +
1061D VAL* 1.3 80.8 - - - +
1063D TYR* 1.3 70.9 + - - +
1083D CYS* 3.6 1.7 - - - -
1084D MET* 2.7 54.9 + - + +
1086D ILE* 3.9 26.7 - - + -
1098D TRP* 4.9 0.7 - - + -
1114D LEU* 4.1 20.6 - - + -
1115D GLY 3.2 23.1 - - - +
1116D LEU* 4.2 7.0 - - + -
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Residues in contact with TYR1063 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1061D VAL* 3.9 5.2 - - + +
1062D ILE* 1.3 75.7 - - - +
1064D ALA* 1.3 63.8 + - - +
1065D LEU* 4.0 0.6 - - + +
1081D GLY 4.1 6.7 - - - +
1082D ASP 3.2 6.3 - - - +
1083D CYS* 3.5 41.1 - - + -
1114D LEU* 3.3 7.5 - - - -
1115D GLY 2.8 38.7 + - - +
1116D LEU 3.4 19.3 - - - -
1117D TYR* 3.6 8.7 - + - +
1118D PRO* 3.7 47.1 - - + -
1201D EDO 3.3 37.9 + - - -
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Residues in contact with ALA1064 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1063D TYR* 1.3 72.2 - - - +
1065D LEU* 1.3 62.2 + - - +
1066D TRP 3.5 8.5 - - - +
1078D MET* 3.7 30.1 - - + -
1079D LYS 3.5 21.1 - - - +
1080D GLU* 4.2 0.3 - - - +
1081D GLY* 2.7 30.0 + - - -
1082D ASP* 3.0 16.2 + - + +
1084D MET* 4.9 2.1 - - - +
1113D LEU 3.9 4.9 - - - -
1114D LEU* 4.2 4.6 - - + +
1118D PRO* 5.6 0.5 - - - +
1119D ARG* 5.6 0.3 + - - +
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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