Contacts of the strand formed by residues 1090 - 1095 (chain B) in PDB entry 3PFS
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 TYR1090 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1081B TRP* 3.6 4.8 - - - -
1082B ALA* 2.8 33.9 + - - +
1087B TYR* 4.6 15.8 - + + -
1088B PRO* 3.3 46.4 - - + +
1089B SER* 1.3 72.4 - - - +
1091B PRO* 1.3 75.2 - - + +
1092B ALA 3.7 0.2 + - - -
1138B PHE* 3.6 26.1 - + + -
1175B ILE* 4.0 15.1 - - - +
1178B SER* 3.8 25.0 + - - -
1179B VAL* 3.4 32.5 - - + +
1182B ALA* 4.7 7.0 - - + -
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Residues in contact with PRO1091 (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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1080B VAL 3.5 8.1 - - - +
1081B TRP* 3.6 21.3 - - + -
1090B TYR* 1.3 94.0 - - + +
1092B ALA* 1.3 61.4 + - - +
1138B PHE* 3.5 10.7 - - - -
1139B PHE* 3.5 16.6 + - + +
1156B LEU* 3.6 16.8 - - + -
1179B VAL* 4.2 3.8 - - + +
1182B ALA* 3.7 26.5 - - + +
1183B TYR* 3.7 27.1 - - + +
1186B ALA* 4.1 9.4 - - + -
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Residues in contact with ALA1092 (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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1079B LEU* 3.5 8.8 - - - +
1080B VAL* 2.9 32.6 + - + -
1082B ALA* 4.0 18.4 - - + -
1091B PRO* 1.3 76.6 - - - +
1093B LEU* 1.3 60.8 + - - +
1136B VAL* 4.0 11.9 - - + -
1137B LEU 3.2 20.4 - - - +
1138B PHE* 3.9 12.3 - - + -
1139B PHE* 3.8 11.1 - - - -
1156B LEU* 4.8 0.2 - - - +
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Residues in contact with LEU1093 (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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1077B LEU* 3.7 17.9 - - + +
1078B GLU 3.6 1.6 - - - +
1079B LEU* 3.5 20.2 - - + -
1080B VAL* 4.8 0.2 - - - -
1092B ALA* 1.3 73.4 - - - +
1094B ILE* 1.3 64.0 + - - +
1095B ILE* 3.7 21.7 + - + +
1111B ILE* 4.0 19.3 - - + -
1136B VAL* 3.2 6.0 - - - -
1137B LEU* 2.8 35.1 + - + +
1139B PHE* 3.6 17.3 - - + -
1143B ARG* 4.5 11.9 - - - +
1189B HIS* 3.2 44.6 - - + +
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Residues in contact with ILE1094 (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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1074B LEU* 4.0 22.7 - - + +
1075B GLU 3.4 32.5 - - - +
1076B PRO* 4.0 3.6 - - + -
1077B LEU* 2.7 31.1 + - - -
1078B GLU* 3.0 16.7 + - + +
1080B VAL* 3.6 26.2 - - + -
1093B LEU* 1.3 71.6 - - - +
1095B ILE* 1.3 68.1 + - - +
1134B PHE* 4.2 26.9 - - + -
1135B LEU 3.5 5.2 - - - +
1136B VAL* 3.9 22.9 - - + -
1153B VAL* 4.4 2.2 - - + -
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Residues in contact with ILE1095 (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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1076B PRO* 4.9 0.2 - - - -
1077B LEU* 4.0 12.6 - - + +
1093B LEU* 3.8 13.9 - - + +
1094B ILE* 1.3 89.9 - - - +
1096B ASP* 1.3 72.5 + - - +
1097B PRO* 3.3 9.0 - - - +
1099B MET* 3.5 25.4 - - - -
1111B ILE* 3.9 26.7 - - + -
1114B PRO* 3.9 5.8 - - + -
1135B LEU* 2.8 27.5 + - + +
1137B LEU* 3.8 18.2 - - + +
1145B TRP* 3.6 32.8 - - + -
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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