Contacts of the strand formed by residues 1087 - 1094 (chain D) in PDB entry 6X34
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 ARG1087 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1086D GLY* 1.3 74.8 - - - +
1088D TRP* 1.3 61.1 + - - +
1153D ILE* 3.3 17.5 - - - +
1154D ASP* 4.4 8.1 - - + -
1221D GLU 5.5 2.5 - - - +
1222D GLY 4.8 2.9 - - - +
1223D PHE* 3.7 25.4 - - + +
1224D GLU* 3.1 21.2 + - - +
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Residues in contact with TRP1088 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083D VAL* 5.9 4.5 - - + -
1087D ARG* 1.3 75.6 - - - +
1089D TYR* 1.3 61.1 + - - +
1104D TRP* 3.5 24.0 - - + -
1152D MET* 3.3 24.9 - - - +
1153D ILE* 3.6 10.7 + - + +
1223D PHE* 3.7 6.2 - - - +
1224D GLU 3.2 10.5 - - - +
1225D PRO 5.2 0.2 - - - +
1226D PHE* 3.9 27.8 - - + -
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Residues in contact with TYR1089 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1088D TRP* 1.3 76.4 - - - +
1090D PHE* 1.3 58.4 + - - +
1091D GLU* 3.8 17.3 + - + +
1104D TRP* 4.2 2.0 - - - -
1150D GLY* 4.4 13.5 - - - -
1151D CYS 3.3 14.6 - - - -
1152D MET* 4.3 10.8 - - + -
1163D THR* 4.3 22.9 - - + +
1166D GLY* 6.0 0.2 - - - -
1203D ASN* 5.2 2.1 - - - +
1204D LEU 5.3 4.9 - - - +
1205D GLY* 5.5 1.9 + - - -
1211D LEU* 3.6 32.4 - - + +
1212D ARG 5.8 0.9 - - - -
1213D PHE* 3.7 23.1 + - - +
1214D PHE* 3.6 42.6 - + + -
1218D GLY* 5.9 1.6 - - - -
1223D PHE* 4.3 5.8 - - + +
1224D GLU 3.7 3.8 + - - -
1225D PRO* 4.4 9.7 - - + +
1226D PHE* 4.6 11.5 + - - +
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Residues in contact with PHE1090 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089D TYR* 1.3 75.7 - - - +
1091D GLU* 1.3 64.7 + - - +
1092D PHE* 3.7 13.7 - + + -
1102D VAL* 3.5 32.5 - - + -
1103D GLY* 5.1 4.3 - - - -
1104D TRP* 3.6 26.0 - + + -
1150D GLY* 3.3 2.6 - - - -
1151D CYS* 2.5 49.6 + - + +
1190D PRO* 3.6 31.6 - - + -
1191D VAL 4.0 8.5 - - - -
1192D CYS* 3.5 28.9 - - - -
1202D LEU* 5.0 3.6 - - + -
1203D ASN 3.8 21.5 - - - -
1204D LEU* 5.5 2.7 - - - -
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Residues in contact with GLU1091 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1089D TYR* 3.8 21.4 + - + +
1090D PHE* 1.3 79.0 - - - +
1092D PHE* 1.3 61.9 + - - +
1148D VAL* 6.4 0.9 - - + -
1149D VAL 3.8 4.0 - - - +
1150D GLY* 4.5 1.8 - - - -
1203D ASN* 3.1 57.1 + - + +
1210D SER 5.3 1.8 - - - +
1211D LEU* 5.2 2.5 - - + -
1212D ARG* 6.1 3.8 - - + +
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Residues in contact with PHE1092 (chain D).
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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839D LEU* 5.4 2.7 - - + -
1090D PHE* 3.7 14.4 - + + -
1091D GLU* 1.3 74.3 - - - +
1093D GLU* 1.3 55.6 + - - +
1094D ALA* 4.0 10.9 + - + -
1100D MET* 3.7 33.0 - - + -
1101D ARG 5.8 2.2 - - - -
1102D VAL* 4.0 12.3 - - + -
1143D TRP* 4.0 26.0 - + - -
1148D VAL* 3.3 2.7 - - - +
1149D VAL* 2.6 48.8 + - + +
1192D CYS* 3.9 33.7 - - + -
1193D SER 4.6 8.7 - - - -
1200D GLY* 4.3 11.7 - - - -
1201D HIS 3.2 26.9 - - - -
1202D LEU* 4.2 3.4 - - + -
1203D ASN* 5.4 0.2 - - - -
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Residues in contact with GLU1093 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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835D ARG* 4.8 16.8 - - - +
1091D GLU 4.4 0.2 - - - -
1092D PHE* 1.3 72.6 - - - +
1094D ALA* 1.3 64.6 + - - +
1095D VAL* 3.6 1.2 + - - +
1146D GLY 5.7 1.1 - - - +
1147D ASP 3.6 8.3 - - - +
1148D VAL* 3.8 19.3 - - + -
1201D HIS* 2.9 43.6 + - + +
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Residues in contact with ALA1094 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1092D PHE* 4.0 10.5 - - + -
1093D GLU* 1.3 72.6 - - - +
1095D VAL* 1.3 63.0 + - - +
1096D THR 3.9 13.2 - - - +
1097D THR* 5.3 2.0 - - - -
1100D MET* 3.7 28.0 - - - -
1143D TRP* 4.7 12.3 - - + -
1144D GLN 5.7 2.9 - - - +
1145D SER 3.1 15.8 - - - +
1146D GLY* 4.5 2.8 - - - -
1147D ASP 3.6 11.6 + - - +
1200D GLY* 3.9 7.6 - - - -
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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