Contacts of the strand formed by residues 1092 - 1096 (chain B) in PDB entry 1FP7
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 VAL1092 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1026B LEU* 5.7 1.1 - - - +
1082B THR* 4.0 13.2 - - + -
1085B LEU* 3.4 32.8 - - + -
1086B ALA* 3.2 39.4 - - + +
1090B LYS 3.0 4.9 + - - -
1091B ARG* 1.3 74.4 - - - +
1093B MET* 1.3 88.3 + - - +
1266B THR* 4.0 12.0 - - - +
1267B PRO* 4.3 6.6 - - - +
1295B ALA* 3.8 1.5 - - - +
1297B TYR* 3.4 23.3 - - + +
1299B VAL* 3.7 7.4 - - + -
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Residues in contact with MET1093 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026B LEU* 4.0 24.5 - - + -
1082B THR* 3.9 4.1 + - - -
1092B VAL* 1.3 81.2 - - - +
1094B VAL* 1.3 68.4 + - - +
1259B LEU* 4.0 19.3 - - + -
1267B PRO* 3.1 46.7 - - + +
1269B PHE* 4.3 17.9 - - + -
1291B ALA* 4.1 30.7 - - + +
1294B LEU* 4.2 12.6 - - + -
1295B ALA* 4.2 9.2 - - + -
1297B TYR 3.5 6.6 + - - +
1298B VAL* 4.8 2.7 - - + -
1299B VAL* 3.1 31.1 + - - +
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Residues in contact with VAL1094 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1078B SER 4.0 10.5 - - - +
1079B VAL* 4.5 12.8 - - + -
1082B THR* 2.9 37.5 - - + +
1093B MET* 1.3 76.7 - - - +
1095B CYS* 1.3 58.7 + - - +
1096B LEU* 3.6 15.4 + - + +
1119B VAL* 5.1 4.0 - - + -
1262B THR* 5.0 4.3 - - - +
1266B THR 4.5 2.0 - - - +
1267B PRO 3.3 3.3 + - - +
1268B ALA* 3.3 35.6 - - + +
1269B PHE* 2.6 36.3 + - - +
1299B VAL 3.5 14.6 - - - +
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Residues in contact with CYS1095 (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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1094B VAL* 1.3 72.3 - - - +
1096B LEU* 1.3 66.7 + - - +
1269B PHE* 3.2 16.8 - - - -
1283B ASN* 2.8 27.6 + - - +
1287B ALA* 3.8 5.2 - - - -
1288B THR* 3.2 56.8 - - + +
1291B ALA* 3.6 19.5 - - - -
1298B VAL* 4.2 4.2 - - + +
1299B VAL 3.5 7.7 + - - -
1300B THR* 3.4 13.4 + - - +
1301B GLU* 4.1 1.2 + - - +
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Residues in contact with LEU1096 (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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1075B THR* 4.5 13.0 - - + -
1078B SER* 4.8 7.2 - - - -
1079B VAL* 4.3 17.5 - - + -
1094B VAL* 4.4 15.3 - - + +
1095B CYS* 1.3 82.5 - - - +
1097B ARG* 1.3 68.5 + - - +
1112B ALA 4.6 4.7 - - - +
1119B VAL* 4.1 26.0 - - + -
1268B ALA* 6.0 0.4 - - + -
1269B PHE 2.8 14.5 + - - +
1270B ILE* 4.3 10.5 - - + -
1271B HIS 3.6 15.4 + - - +
1283B ASN* 2.8 22.0 - - - +
1299B VAL 4.7 6.5 - - - +
1301B GLU* 3.6 32.5 - - + +
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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
------------------------------------------------------------
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