Contacts of the strand formed by residues 1136 - 1142 (chain A) in PDB entry 4ZTZ
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 GLU1136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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875A LYS* 5.0 7.1 + - - -
889A ALA 3.2 23.0 - - - +
890A ASP* 3.3 21.6 - - + +
1109A LEU* 5.7 0.2 - - - +
1132A SER* 3.7 1.6 - - - -
1133A ILE* 2.9 48.2 + - + +
1134A HIS 3.9 3.1 - - - +
1135A ASP* 1.3 80.2 - - - +
1137A VAL* 1.3 65.7 + - - +
1138A ARG* 2.6 44.5 + - - -
1184A ASP* 3.5 11.1 - - - +
1190A ARG 4.0 3.5 - - - +
1191A LYS* 5.1 3.6 - - - +
24P DOC 5.4 6.4 + - - +
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Residues in contact with VAL1137 (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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887A VAL 4.5 0.2 - - - +
888A GLY* 3.1 2.3 - - - -
889A ALA 2.9 33.9 + - - +
1109A LEU* 6.1 2.2 - - + -
1112A MET* 3.7 37.5 - - + -
1113A LEU* 4.4 12.6 - - + -
1116A MET* 6.0 0.2 - - + -
1130A CYS* 5.2 1.6 - - - -
1131A ILE 3.7 7.6 - - - +
1132A SER* 4.0 18.4 - - - +
1135A ASP 4.8 1.8 - - - +
1136A GLU* 1.3 79.4 - - - +
1138A ARG* 1.3 65.2 + - - +
1139A TYR* 3.9 27.1 - - + -
1153A LEU* 4.8 9.6 - - + +
1180A PHE* 5.6 0.2 - - + -
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Residues in contact with ARG1138 (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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875A LYS* 5.9 1.6 - - - +
886A LEU* 4.4 17.9 - - + +
887A VAL 4.3 1.6 - - - +
888A GLY* 3.5 23.1 - - - +
889A ALA 4.0 0.2 - - - +
1130A CYS* 4.0 0.3 - - - -
1131A ILE* 2.9 55.6 + - + +
1133A ILE* 4.5 9.8 - - + +
1136A GLU* 2.6 44.2 + - - -
1137A VAL* 1.3 85.8 - - - +
1139A TYR* 1.3 64.3 + - - +
1184A ASP* 3.2 25.3 + - - +
1186A ASP* 4.9 1.6 + - - -
1189A LEU* 4.1 26.3 - - + +
1190A ARG* 3.1 38.0 + - - +
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Residues in contact with TYR1139 (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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429A GLU* 3.2 26.9 + - - -
886A LEU* 3.2 5.8 - - - +
887A VAL 2.9 37.9 + - - +
1113A LEU* 3.7 18.9 + - - +
1116A MET* 3.2 55.2 - - + +
1120A PHE* 4.5 15.0 - + + -
1127A GLY 4.9 0.4 - - - +
1128A ARG* 3.5 18.4 - - + -
1129A PHE 3.2 17.9 - - - -
1130A CYS* 3.6 13.9 - - + -
1131A ILE* 4.7 1.1 - - - -
1137A VAL* 3.9 18.8 - - + -
1138A ARG* 1.3 76.0 - - - +
1140A LEU* 1.3 59.4 + - - +
1141A VAL* 3.2 12.7 + - + +
1153A LEU* 4.4 8.5 - - + -
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Residues in contact with LEU1140 (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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284A ILE* 5.1 8.1 - - + +
434A TYR* 5.0 11.7 - - + -
436A PRO* 4.2 22.7 - - + -
880A ALA* 3.8 28.3 - - + -
881A PRO* 4.5 8.7 - - + -
884A TYR* 4.2 25.2 - - + -
885A THR 4.2 3.4 - - - -
886A LEU* 4.1 15.9 - - + -
1127A GLY* 3.3 24.4 + - - +
1129A PHE* 3.1 28.7 + - + +
1131A ILE* 4.3 10.4 - - + +
1138A ARG 4.3 0.2 + - - -
1139A TYR* 1.3 68.8 - - - +
1141A VAL* 1.3 64.7 + - - +
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Residues in contact with VAL1141 (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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884A TYR* 3.1 15.1 - - - +
885A THR 2.8 26.0 + - - +
887A VAL* 3.7 26.7 - - + -
1120A PHE* 4.5 1.3 - - + -
1125A ILE* 3.8 9.2 - - + -
1126A ASP 3.2 23.1 - - - +
1127A GLY 4.1 3.6 - - - +
1139A TYR* 3.6 22.7 - - + +
1140A LEU* 1.3 74.6 - - - +
1142A ARG* 1.3 67.2 + - - +
1145A ASP* 3.3 26.5 - - + +
1149A ALA* 3.8 16.8 - - + -
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Residues in contact with ARG1142 (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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822A PRO* 5.7 1.2 - - - +
824A ALA* 5.3 12.1 - - - +
825A VAL* 5.2 4.9 - - - +
883A GLY* 3.3 23.8 + - - +
884A TYR* 2.9 39.1 + - + +
885A THR* 3.5 9.7 - - - +
1126A ASP* 3.2 32.1 + - + +
1141A VAL* 1.3 76.7 - - - +
1143A GLU* 1.3 67.8 + - - +
1144A GLU* 2.4 42.8 + - + +
1145A ASP* 3.2 40.8 + - + +
1146A ARG* 3.3 10.7 + - - +
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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