Contacts of the strand formed by residues 1137 - 1142 (chain A) in PDB entry 6Q6Q
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 SER1137 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1029A LEU* 4.2 4.7 - - - +
1030A VAL 3.4 4.5 - - - -
1031A HIS* 2.9 37.0 + - - -
1106A LEU* 4.0 0.2 - - - -
1109A ARG* 3.2 8.5 + - - -
1135A ASN* 2.7 35.4 - - - +
1136A LEU* 1.3 79.6 - - - +
1138A ALA* 1.3 61.4 + - - +
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Residues in contact with ALA1138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A LEU* 3.3 5.8 - - - +
1030A VAL 3.0 32.1 + - - -
1102A ALA* 4.0 14.5 - - + +
1105A THR* 4.1 11.9 - - + -
1106A LEU* 3.7 27.1 - - + +
1109A ARG* 3.8 13.5 - - - +
1137A SER* 1.3 78.1 + - - +
1139A VAL* 1.3 64.2 + - - +
1140A GLY 4.1 0.5 + - - -
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Residues in contact with VAL1139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027A ALA* 5.3 4.5 - - + -
1028A ALA 3.4 7.9 - - - +
1029A LEU* 3.7 21.3 - - + -
1101A ASP* 3.7 7.8 - - - +
1102A ALA* 3.9 5.8 - - - +
1105A THR* 4.8 4.9 + - - +
1138A ALA* 1.3 74.4 - - - +
1140A GLY* 1.3 73.3 + - - +
1141A TYR* 5.0 7.5 - - + +
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Residues in contact with GLY1140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1027A ALA* 3.3 4.2 - - - +
1028A ALA 2.8 33.3 + - - +
1098A ALA* 3.2 22.9 - - - -
1101A ASP* 3.5 6.1 - - - -
1102A ALA* 3.5 13.0 - - - +
1139A VAL* 1.3 79.2 - - - +
1141A TYR* 1.3 64.2 + - - +
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Residues in contact with TYR1141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1025A GLN* 2.5 48.8 + - + +
1026A ALA 3.5 12.1 - - - -
1027A ALA* 4.1 13.9 - - + -
1098A ALA* 3.9 5.7 + - - +
1101A ASP* 3.2 26.2 + - - +
1139A VAL* 5.0 7.4 - - + +
1140A GLY* 1.3 75.3 - - - +
1142A PHE* 1.3 63.9 + - - +
1143A ARG* 4.0 30.9 - - + +
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Residues in contact with PHE1142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1024A GLY 4.2 1.8 - - - -
1025A GLN* 3.4 2.8 - - - +
1026A ALA 2.9 32.1 + - - +
1094A LEU* 4.0 19.3 - - + +
1097A LEU* 3.5 52.5 - - + -
1098A ALA* 4.2 7.6 - - - +
1141A TYR* 1.3 76.9 - - - +
1143A ARG* 1.3 64.4 + - - +
1144A GLY* 3.2 40.4 + - - -
1145A TYR* 3.8 24.9 - + - -
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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