Contacts of the strand formed by residues 1106 - 1110 (chain B) in PDB entry 1BRW
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 VAL1106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079B VAL 3.7 8.3 - - - +
1080B ASP* 5.7 0.9 - - - -
1096B GLY* 4.0 15.3 - - - +
1099B VAL* 3.9 24.2 - - + -
1100B ALA* 4.1 5.8 - - + -
1104B VAL* 3.6 16.6 - - + +
1105B PRO* 1.3 72.5 - - - +
1107B ALA* 1.3 62.4 + - - +
1108B LYS* 3.9 21.3 - - + +
1143B VAL* 3.8 7.0 - - - +
1147B GLY 3.1 7.3 + - - -
1148B ILE* 3.2 23.1 - - + -
1149B ALA 2.9 27.8 + - - +
1150B ILE* 4.9 3.6 - - + -
1279B MET* 4.9 12.8 - - + -
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Residues in contact with ALA1107 (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 LEU* 3.8 29.2 - - + -
1078B LYS* 4.9 3.6 - - + -
1079B VAL 3.3 8.9 + - - +
1080B ASP* 3.3 24.8 - - - +
1105B PRO 4.0 0.8 + - - -
1106B VAL* 1.3 72.5 - - - +
1108B LYS* 1.3 58.3 + - - +
1139B PHE* 3.7 23.1 - - + -
1143B VAL* 4.1 12.8 - - + -
1191B ALA* 4.4 4.9 - - - +
1193B ALA* 4.3 7.2 - - + +
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Residues in contact with LYS1108 (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 ASP* 3.6 12.3 - - - +
1081B LYS* 2.7 35.6 + - + +
1082B HIS* 3.4 7.7 - - - -
1092B THR* 3.7 31.2 - - + +
1095B LEU* 6.3 1.1 - - + -
1106B VAL* 4.2 13.9 - - + -
1107B ALA* 1.3 74.3 - - - +
1109B MET* 1.3 77.3 + - - +
1110B SER* 3.1 16.6 - - - +
1139B PHE* 3.6 4.2 - - - -
1149B ALA 2.9 14.3 + - - +
1150B ILE* 3.3 11.4 - - + -
1151B ILE* 3.0 28.3 + - - +
1191B ALA* 5.7 0.2 - - - -
2002B PO4 2.9 24.3 + - - -
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Residues in contact with MET1109 (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 ASP* 4.7 1.2 + - - -
1082B HIS* 3.6 4.5 - - - -
1108B LYS* 1.3 94.8 + - - +
1110B SER* 1.3 62.1 + - - +
1139B PHE* 5.0 3.4 - - + -
1151B ILE* 3.3 19.5 - - + +
1152B GLY 4.6 1.3 - - - +
1153B GLN* 4.3 18.8 - - - +
1157B LEU* 3.5 41.7 - - + -
1158B THR* 4.2 8.3 - - - +
1187B LYS* 3.3 52.6 - - + +
1188B LYS* 3.3 14.1 + - - +
1190B ALA* 4.4 3.1 - - + -
1191B ALA* 4.2 17.0 - - + +
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Residues in contact with SER1110 (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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1082B HIS* 4.5 3.4 - - - -
1108B LYS* 3.1 18.2 - - - -
1109B MET* 1.3 72.1 - - - +
1111B GLY* 1.3 59.8 + - - +
1120B THR* 3.8 15.2 - - - +
1121B ILE* 3.4 26.7 - - - +
1150B ILE* 3.8 9.8 - - - +
1151B ILE 2.7 8.6 + - - -
1152B GLY* 3.6 5.5 - - - -
1153B GLN* 3.3 18.4 + - - +
1187B LYS* 4.3 8.6 - - - +
2002B PO4 3.0 22.9 + - - -
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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