Contacts of the strand formed by residues 1026 - 1031 (chain A) in PDB entry 3U9Y
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 GLU1026 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1009A TYR* 2.6 29.7 + - - +
1013A ARG* 2.9 32.2 + - - -
1023A HIS* 5.1 0.2 - - - -
1024A ALA* 4.1 12.8 - - + +
1025A ASN* 1.3 75.5 - - - +
1027A ARG* 1.3 69.1 + - - +
1028A MET* 5.9 0.2 - - - -
1100A ARG* 3.0 41.2 + - + +
1101A VAL 3.2 7.2 - - - +
1102A THR* 4.3 0.7 - - - +
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Residues in contact with ARG1027 (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 ASN* 2.9 36.3 + - - +
1026A GLU* 1.3 81.4 + - - +
1028A MET* 1.3 64.9 + - - +
1029A LEU* 3.8 26.0 - - + -
1063A GLU* 4.0 6.4 + - - -
1099A CYS 3.4 0.9 - - - +
1100A ARG* 3.4 4.2 - - - -
1101A VAL* 2.8 32.5 + - - +
1103A LEU* 3.3 27.4 - - + +
1139A TYR* 3.2 27.3 + - + -
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Residues in contact with MET1028 (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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971A GLU* 5.5 2.3 - - - +
1026A GLU* 6.2 0.2 - - + -
1027A ARG* 1.3 75.7 - - - +
1029A LEU* 1.3 68.5 + - - +
1030A PHE* 5.5 0.7 - - - -
1063A GLU* 5.7 0.5 - - - +
1098A PHE* 3.4 51.6 - - + +
1099A CYS 3.2 16.4 - - - -
1100A ARG* 3.7 45.5 - - - +
1150A GLU* 4.3 7.0 - - + +
1151A TYR* 4.0 22.0 - - + -
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Residues in contact with LEU1029 (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 ARG* 3.8 20.6 - - + -
1028A MET* 1.3 82.6 - - - +
1030A PHE* 1.3 62.5 + - - +
1061A PHE* 3.7 26.6 - - + -
1062A ALA 3.9 6.3 - - - +
1063A GLU* 3.7 31.4 - - + +
1098A PHE* 3.9 6.0 - - - -
1099A CYS* 2.7 44.0 + - - +
1101A VAL* 4.0 24.5 - - + -
1103A LEU* 4.6 1.1 - - + -
1139A TYR* 3.6 33.2 - - + -
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Residues in contact with PHE1030 (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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968A VAL 5.5 0.2 - - - -
971A GLU* 3.7 30.3 - - + -
972A MET* 3.9 30.1 - - + -
975A THR* 3.6 11.0 - - - -
1028A MET 5.5 0.7 - - - -
1029A LEU* 1.3 74.2 - - - +
1031A HIS* 1.3 60.6 + - - +
1061A PHE* 3.3 7.9 - - - +
1062A ALA 2.9 41.8 + - - +
1063A GLU* 3.6 19.7 - - - -
1065A SER* 3.8 13.0 - - - -
1068A SER* 3.1 22.7 + - - +
1096A LEU* 4.5 5.8 - - + -
1097A LEU 3.3 9.6 - - - -
1098A PHE* 3.3 39.9 - + + -
1153A ILE* 4.3 2.5 - - + -
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Residues in contact with HIS1031 (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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1030A PHE* 1.3 75.8 - - - +
1032A GLY* 1.3 58.1 + - - +
1033A SER* 3.5 23.0 + - - -
1036A VAL* 4.6 1.5 - - + +
1039A ILE* 3.6 26.3 - - + +
1044A PHE* 3.8 12.5 - + - -
1059A ILE* 4.5 0.7 - - + -
1060A TYR 2.8 25.6 + - - -
1061A PHE* 3.7 16.2 - - + -
1096A LEU* 3.7 4.3 - - - +
1097A LEU* 2.9 38.8 + - + +
1099A CYS* 4.2 10.1 - - - -
1165A 09L 3.4 49.3 + + - -
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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