Contacts of the helix formed by residues 1128 - 1135 (chain u) in PDB entry 6FF7
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 VAL1128 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1090u PRO* 5.5 4.3 - - + +
1094u LEU* 6.0 7.0 - - + -
1116u ILE* 5.2 3.6 - - + +
1119u VAL* 5.2 7.6 - - + +
1120u ALA* 4.8 24.9 - - + +
1125u PRO* 5.7 0.6 - - - +
1126u PHE* 4.5 0.6 - - - +
1127u THR* 1.3 81.5 - - - +
1129u LEU* 1.3 57.6 + - - +
1130u PRO 3.7 1.3 - - - -
1131u ALA* 3.8 8.1 + - - +
1132u LEU* 3.2 28.4 + - + +
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Residues in contact with LEU1129 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126u PHE* 4.7 16.5 - - - +
1127u THR 3.7 1.4 - - - +
1128u VAL* 1.3 75.7 - - - +
1130u PRO* 1.4 60.5 - - - +
1132u LEU* 3.7 6.4 - - - +
1133u MET* 2.9 28.6 + - - +
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Residues in contact with PRO1130 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5288 ILE* 5.2 18.1 - - + +
5318 THR* 5.7 4.9 - - - -
5338 ILE* 4.4 21.2 - - + +
5718 LEU* 6.4 1.3 - - + -
1126u PHE 5.8 2.0 - - - +
1127u THR 5.4 1.2 - - - -
1128u VAL 3.7 0.4 - - - -
1129u LEU* 1.4 75.7 - - - +
1131u ALA* 1.3 59.4 + - - +
1133u MET* 3.3 8.2 + - + +
1134u ASN* 2.9 26.6 + - - +
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Residues in contact with ALA1131 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5338 ILE* 5.2 6.0 - - + +
5378 ARG* 6.2 3.6 - - + -
1094u LEU* 6.2 4.3 - - + -
1127u THR 5.9 1.3 - - - +
1128u VAL* 3.8 8.5 + - - +
1129u LEU 3.4 0.2 - - - -
1130u PRO* 1.3 75.2 - - - +
1132u LEU* 1.3 60.2 + - - +
1134u ASN* 3.5 9.5 - - + +
1135u GLU* 2.9 30.7 + - - +
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Residues in contact with LEU1132 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1128u VAL* 3.2 19.8 + - + +
1129u LEU* 3.7 8.5 - - - +
1130u PRO 3.3 0.2 - - - -
1131u ALA* 1.3 79.8 - - - +
1133u MET* 1.3 60.1 + - - +
1135u GLU* 3.9 7.2 + - - +
1136u TYR* 4.2 3.5 + - - +
1147u VAL* 3.8 27.3 - - + +
1150u SER* 6.3 3.1 - - - -
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Residues in contact with MET1133 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5228 PHE* 5.6 3.1 - - - +
5288 ILE* 5.8 7.0 - - + -
1129u LEU 2.9 17.8 + - - +
1130u PRO* 3.5 8.3 - - + +
1132u LEU* 1.3 76.1 - - - +
1134u ASN* 1.3 63.8 + - - +
1135u GLU 3.5 0.3 + - - -
1136u TYR* 3.6 17.2 + - - +
1137u ARG* 4.5 1.4 + - - +
1172u LEU* 6.2 6.1 - - + -
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Residues in contact with ASN1134 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5338 ILE* 5.6 3.1 - - + +
5348 GLN* 5.6 8.5 - - + -
5378 ARG* 5.0 15.9 - - + -
1130u PRO 2.9 17.1 + - - +
1131u ALA* 3.1 11.8 + - - +
1133u MET* 1.3 78.4 - - - +
1135u GLU* 1.3 62.3 + - - +
1137u ARG* 3.2 22.9 + - - +
1138u VAL 4.3 0.9 + - - -
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Residues in contact with GLU1135 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1098u LEU* 5.6 11.2 - - + -
1131u ALA 2.9 14.9 + - - +
1132u LEU* 3.9 7.4 + - - +
1133u MET 3.3 0.8 - - - -
1134u ASN* 1.3 74.2 - - - +
1136u TYR* 1.3 63.9 + - - +
1138u VAL* 3.1 25.8 + - + +
1143u VAL* 4.7 19.4 - - + +
1144u GLN 5.3 0.2 + - - -
1147u VAL* 5.1 7.9 - - + -
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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