Contacts of the strand formed by residues 1097 - 1102 (chain B) in PDB entry 4ESR
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 GLN1097 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1070B LEU* 3.7 10.7 - - + +
1071B THR 5.3 1.4 + - - -
1092B SER* 3.2 4.9 + - - -
1093B ILE* 3.0 55.8 + - + +
1094B GLY 3.0 18.8 + - - +
1095B LYS* 3.8 16.2 - - + +
1096B GLY* 1.3 71.1 - - - +
1098B GLU* 1.3 61.6 + - - +
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Residues in contact with GLU1098 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1055A THR* 3.5 35.0 + - - +
1077A ILE* 4.9 6.0 - - - +
1079A ARG* 2.9 36.1 + - - +
1069B GLU 4.3 0.2 - - - +
1070B LEU* 3.7 12.3 - - - +
1081B PHE* 3.6 23.0 - - + -
1090B TYR* 2.7 29.5 + - + +
1091B GLY 3.1 18.2 - - - +
1092B SER* 4.0 6.2 + - - +
1096B GLY* 3.5 5.1 + - - +
1097B GLN* 1.3 75.8 - - - +
1099B GLY* 1.3 59.3 + - - +
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Residues in contact with GLY1099 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079A ARG* 4.0 2.5 - - - -
1068B ASP 3.5 11.4 - - - -
1070B LEU* 3.8 9.7 - - - +
1090B TYR* 3.4 20.6 - - - -
1091B GLY 3.0 28.4 + - - +
1098B GLU* 1.3 77.8 - - - +
1100B TYR* 1.3 64.4 + - - -
1101B PHE* 3.7 5.2 - - - -
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Residues in contact with TYR1100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081A PHE* 5.4 5.6 - + - -
1095A LYS* 5.0 5.5 - - - +
1096A GLY 5.0 3.1 + - - -
1062B TYR* 4.9 0.2 - - - -
1066B ARG* 5.2 3.6 - - - +
1068B ASP* 2.9 47.3 + - + +
1069B GLU* 3.3 16.3 - - + +
1070B LEU 2.9 22.7 + - - +
1082B PHE* 3.7 22.1 - + - -
1084B ASP* 3.2 38.1 + - + -
1088B TRP* 4.0 25.2 - + + -
1089B TRP 3.2 16.4 - - - -
1090B TYR* 3.8 18.6 - + + -
1099B GLY* 1.3 72.9 - - - -
1101B PHE* 1.3 57.4 + - - +
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Residues in contact with PHE1101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1056B VAL* 4.8 0.4 - - + -
1070B LEU* 4.2 19.7 - - + +
1072B ILE* 4.2 17.9 - - + -
1078B ILE* 3.6 28.3 - - + -
1080B VAL* 4.3 5.4 - - + -
1088B TRP* 3.4 8.5 - - - -
1089B TRP* 2.9 70.7 + + + +
1090B TYR 3.8 4.9 - - - -
1091B GLY 3.6 21.1 - - - -
1099B GLY 3.7 9.6 - - - -
1100B TYR* 1.3 74.3 - - - +
1102B PRO* 1.3 84.6 - - + +
1106B VAL* 3.6 27.6 - - + -
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Residues in contact with PRO1102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1062B TYR* 3.6 35.9 - - + -
1072B ILE* 4.9 0.9 - - + -
1087B ASP 3.4 10.3 - - - +
1088B TRP* 3.6 13.0 - - + -
1101B PHE* 1.3 96.3 - - + +
1103B ALA* 1.3 64.9 + - - +
1104B ASN* 3.6 15.3 - - - +
1105B HIS* 3.0 37.0 + - + +
1106B VAL 4.3 0.2 + - - -
1202B PEG 3.8 17.5 - - - +
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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