Contacts of the strand formed by residues 1094 - 1102 (chain A) in PDB entry YUA9
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 ARG1094 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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986A GLY* 3.0 22.1 + - - -
1069A ASN* 3.1 31.0 + - - +
1072A VAL* 4.3 10.9 - - + +
1073A TYR* 3.5 42.1 + - + +
1087A ARG 3.0 24.2 + - - -
1089A CYS* 3.3 31.5 + - - +
1092A CYS 4.0 5.9 + - - +
1093A HIS* 1.3 73.5 - - - +
1095A GLN* 1.3 66.8 + - - +
1154A THR* 3.3 5.4 - - - +
1155A TYR* 2.8 59.5 + - + +
1157A ILE* 3.5 22.2 - - - +
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Residues in contact with GLN1095 (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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998A GLN* 4.9 1.8 + - - -
1033A SER 5.0 0.7 - - - +
1036A VAL* 4.4 17.2 - - + +
1037A ASN* 3.0 31.9 + - - +
1072A VAL* 3.8 24.5 - - - +
1093A HIS 5.5 1.3 - - - +
1094A ARG* 1.3 83.0 - - - +
1096A LEU* 1.3 59.2 + - - +
1152A LEU* 3.7 33.2 - - + +
1153A ILE 3.1 5.4 - - - +
1154A THR* 3.1 30.2 + - + +
1155A TYR* 3.8 3.8 - - - -
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Residues in contact with LEU1096 (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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972A MET* 4.0 23.8 - - + -
992A TYR* 5.1 0.7 - - - +
1030A PHE* 4.5 7.9 - - + -
1031A HIS 3.5 4.7 - - - +
1032A GLY* 3.4 31.2 - - - +
1036A VAL* 4.9 1.3 - - - -
1065A SER* 3.9 23.6 - - - +
1068A SER* 3.8 19.7 - - - +
1069A ASN* 4.4 1.3 - - + +
1072A VAL* 3.9 11.4 - - + -
1095A GLN* 1.3 72.5 - - - +
1097A LEU* 1.3 68.3 + - - +
1152A LEU* 3.7 6.3 - - - +
1153A ILE* 2.9 38.7 + - + +
1155A TYR* 3.5 25.9 - - + +
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Residues in contact with LEU1097 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1000A VAL* 4.9 0.4 - - + -
1029A LEU 3.9 0.3 - - - +
1030A PHE* 3.3 7.5 - - - +
1031A HIS* 2.8 47.5 + - + +
1036A VAL* 3.8 25.5 - - + +
1039A ILE* 4.0 28.9 - - + -
1040A ILE* 3.3 27.8 - - + -
1044A PHE* 4.3 2.7 - - + -
1096A LEU* 1.3 76.3 - - - +
1098A PHE* 1.3 59.7 + - - +
1099A CYS* 3.5 15.5 - - - -
1149A PRO* 4.1 11.9 - - + -
1151A TYR 3.3 13.5 - - - +
1152A LEU* 3.7 20.4 - - + -
1153A ILE* 4.9 0.4 - - - -
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Residues in contact with PHE1098 (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* 4.1 22.2 - - + -
971A GLU* 3.6 26.9 - - + -
1028A MET* 3.5 58.1 - - + -
1029A LEU 3.7 8.5 - - - -
1030A PHE* 3.5 35.2 - + + -
1096A LEU 4.2 0.2 + - - -
1097A LEU* 1.3 71.4 - - - +
1099A CYS* 1.3 60.1 + - - +
1150A GLU* 3.2 8.3 + - - +
1151A TYR* 3.0 49.4 + + + -
1153A ILE* 3.8 19.9 - - + +
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Residues in contact with CYS1099 (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 3.6 0.3 - - - +
1028A MET* 3.2 10.1 - - - -
1029A LEU 2.8 36.5 + - - +
1031A HIS* 4.1 2.7 - - - -
1044A PHE* 3.8 11.2 - - + -
1061A PHE* 3.7 30.5 - - + -
1097A LEU* 3.5 34.3 - - - -
1098A PHE* 1.3 75.0 - - - +
1100A ARG* 1.3 61.2 + - - +
1101A VAL* 3.7 5.1 + - + +
1148A TYR 3.3 10.8 - - - +
1149A PRO* 3.8 13.0 - - - -
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Residues in contact with ARG1100 (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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1006A TRP* 4.0 13.6 - - - -
1009A TYR* 3.5 18.3 - - + +
1013A ARG* 4.3 2.7 - - - +
1026A GLU* 3.0 52.9 + - + +
1027A ARG 3.5 3.1 - - - -
1028A MET* 3.8 26.8 - - - +
1099A CYS* 1.3 71.6 - - - +
1101A VAL* 1.3 59.2 + - - +
1147A ALA* 3.1 3.6 - - - -
1148A TYR* 2.8 42.6 + - + +
1150A GLU* 2.7 38.0 + - + +
1151A TYR* 5.9 1.2 + - - -
1164A PEG 4.3 6.0 + - - -
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Residues in contact with VAL1101 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1009A TYR* 3.6 3.6 - - - -
1025A ASN 3.8 0.2 - - - +
1026A GLU* 3.2 2.6 - - - -
1027A ARG* 2.8 40.8 + - - +
1029A LEU* 4.1 15.7 - - + -
1061A PHE* 3.7 47.1 - - + -
1099A CYS* 3.8 10.3 - - + +
1100A ARG* 1.3 80.9 - - - +
1102A THR* 1.3 61.8 + - - +
1103A LEU* 3.7 24.4 + - + +
1141A ILE* 3.9 21.5 - - + -
1146A GLN 3.5 7.2 - - - +
1147A ALA* 4.2 1.1 - - + -
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Residues in contact with THR1102 (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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1009A TYR* 2.9 26.1 + - - -
1013A ARG* 3.6 20.4 - - - +
1016A VAL* 3.7 36.1 - - + -
1024A ALA* 3.5 23.2 - - + +
1025A ASN 4.3 0.2 - - - -
1026A GLU* 4.3 2.4 + - - +
1101A VAL* 1.3 74.7 - - - +
1103A LEU* 1.3 59.4 + - - +
1141A ILE* 4.1 1.7 - - - +
1146A GLN* 2.9 46.1 + - + +
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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