Contacts of the strand formed by residues 1091 - 1097 (chain B) in PDB entry 3F66
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 CYS1091 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083B VAL* 5.4 8.1 - - + -
1085B GLY 3.7 6.3 - - - +
1086B ARG* 3.9 35.2 - - - +
1090B GLY* 1.3 75.3 - - - -
1092B VAL* 1.3 61.3 + - - +
1093B TYR* 3.3 37.5 - - + +
1109B VAL 3.7 1.0 - - - +
1110B LYS* 3.3 3.1 - - - -
1111B SER* 3.1 30.1 + - - +
1113B ASN* 5.3 1.2 - - - +
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Residues in contact with VAL1092 (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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2B IHX 3.8 53.2 - - + -
1083B VAL* 3.7 4.7 - - - +
1084B ILE* 2.7 38.0 + - + -
1085B GLY 2.8 22.1 + - - +
1090B GLY 4.7 1.1 - - - +
1091B CYS* 1.3 76.9 - - - +
1093B TYR* 1.3 58.7 + - - +
1108B ALA* 4.1 13.2 - - + -
1109B VAL 3.2 9.2 - - - +
1110B LYS* 4.1 23.3 - - + +
1230B TYR* 4.7 7.4 - - + +
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Residues in contact with TYR1093 (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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1078B VAL* 3.9 13.5 - - + -
1079B HIS 3.7 7.9 - - - +
1080B PHE* 3.5 63.5 - + + -
1082B GLU 3.5 4.3 - - - -
1083B VAL* 4.0 16.8 - - + -
1084B ILE* 3.5 7.9 - - - +
1091B CYS* 3.3 39.7 - - + +
1092B VAL* 1.3 77.0 - - - +
1094B HIS* 1.3 70.3 + - - +
1108B ALA* 3.3 4.7 - - - -
1109B VAL* 2.7 49.6 + - + +
1111B SER* 4.5 12.8 - - - -
1154B LEU* 6.2 0.2 - - + -
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Residues in contact with HIS1094 (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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1078B VAL* 4.1 0.9 - - - +
1079B HIS* 2.8 32.0 + - + +
1082B GLU* 3.1 53.9 + - + -
1083B VAL 4.9 2.0 + - - -
1084B ILE* 3.4 28.3 - - + +
1093B TYR* 1.3 75.6 - - - +
1095B GLY* 1.3 57.7 + - - +
1106B HIS* 2.7 27.5 + + + +
1107B CYS 3.6 4.3 - - - -
1159B TYR* 3.3 34.2 + + - -
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Residues in contact with GLY1095 (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 ILE 3.3 10.3 - - - -
1078B VAL* 4.3 0.7 - - - -
1079B HIS* 3.5 4.2 - - - -
1093B TYR 3.5 0.6 + - - -
1094B HIS* 1.3 75.1 - - - +
1096B THR* 1.3 63.4 + - - -
1106B HIS* 3.5 11.3 - - - -
1107B CYS* 2.8 42.9 + - - +
1109B VAL* 4.0 10.5 - - - -
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Residues in contact with THR1096 (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 LEU* 3.4 4.9 - - - +
1077B ILE* 2.7 51.8 + - + +
1079B HIS* 2.7 27.0 + - - -
1095B GLY* 1.3 73.2 + - - -
1097B LEU* 1.3 63.7 + - - +
1098B LEU* 4.3 2.9 - - + -
1104B LYS* 3.5 48.5 - - + +
1105B ILE 3.5 8.7 - - - +
1106B HIS* 5.2 2.4 - - - -
1107B CYS* 4.0 0.4 - - - -
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Residues in contact with LEU1097 (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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1071B ILE* 3.6 38.1 - - + -
1075B SER* 3.3 17.0 - - - +
1076B LEU* 4.1 9.0 - - + -
1096B THR* 1.3 73.6 - - - +
1098B LEU* 1.3 66.5 + - - +
1104B LYS* 3.5 1.6 - - - -
1105B ILE* 2.7 71.0 + - + +
1107B CYS* 4.0 9.2 - - - -
1143B LEU* 4.6 13.7 - - + -
1156B VAL* 4.2 15.9 - - + -
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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