Contacts of the strand formed by residues 1133 - 1139 (chain A) in PDB entry 2DQZ
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 LEU1133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1124A PRO* 4.0 15.0 - - + -
1125A ALA* 3.8 27.1 - - + +
1131A ASN* 4.4 16.4 - - + +
1132A ARG* 1.3 74.4 - - - +
1134A PRO* 1.3 80.9 - - + +
1162A ASN* 3.1 50.5 - - - +
1163A VAL* 4.4 1.8 - - - +
1164A VAL* 4.6 5.2 - - + +
1209A GLY 3.0 14.5 + - - +
1210A GLY* 3.6 3.6 - - - -
1211A ASN* 2.8 23.8 + - - +
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Residues in contact with PRO1134 (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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1132A ARG 4.6 1.3 - - - +
1133A LEU* 1.3 90.9 - - + +
1135A VAL* 1.3 59.9 + - - +
1162A ASN 4.3 3.1 - - - +
1163A VAL* 3.3 29.8 - - + +
1164A VAL* 3.1 24.1 + - - -
1211A ASN* 4.8 0.2 - - - -
1214A SER* 3.8 23.6 - - - +
1504A ALA* 4.3 15.0 - - + +
1505A ARG* 3.7 31.2 - - + +
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Residues in contact with VAL1135 (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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1133A LEU 3.8 1.1 - - - +
1134A PRO* 1.3 77.7 - - - +
1136A MET* 1.3 64.5 + - - +
1137A VAL* 4.1 14.1 + - + -
1164A VAL* 3.6 7.6 - - + +
1166A VAL* 4.0 25.1 - - + -
1201A VAL* 4.3 5.6 - - + -
1205A ILE* 3.7 29.6 - - + -
1210A GLY* 4.0 2.7 - - - -
1211A ASN 3.7 27.8 - - - +
1214A SER 3.0 10.5 + - - +
1215A VAL* 3.5 10.4 - - + +
1216A THR* 2.8 31.7 + - - +
1504A ALA* 5.2 0.2 - - - +
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Residues in contact with MET1136 (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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1135A VAL* 1.3 76.5 - - - +
1137A VAL* 1.3 63.2 + - - +
1138A TRP 3.8 0.5 + - - -
1157A LEU* 4.3 15.3 - - + -
1163A VAL* 4.2 25.1 - - + -
1164A VAL 2.9 10.7 + - - +
1165A VAL* 3.5 8.7 - - + +
1166A VAL 2.9 25.6 + - - +
1216A THR* 3.4 16.6 - - + -
1218A PHE* 3.4 34.5 - - + -
1244A ILE* 4.6 2.0 - - + -
1500A TRP* 3.9 38.4 - - + +
1501A ALA* 4.4 10.5 - - - -
1504A ALA* 4.1 22.7 - - + -
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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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1135A VAL* 4.1 12.8 - - + -
1136A MET* 1.3 73.6 - - - +
1138A TRP* 1.3 62.7 + - - +
1139A ILE* 3.9 2.3 + - + +
1166A VAL* 3.4 13.2 - - + +
1168A ILE* 3.9 37.2 - - + -
1197A ALA* 5.9 0.9 - - + -
1198A LEU* 4.5 13.2 - - + -
1201A VAL* 4.4 13.7 - - + -
1215A VAL* 4.0 23.6 - - + -
1216A THR 2.8 12.5 + - - +
1217A ILE* 3.5 11.4 - - + +
1218A PHE* 3.0 30.8 + - - +
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Residues in contact with TRP1138 (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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1136A MET 5.2 0.2 - - - +
1137A VAL* 1.3 73.0 - - - +
1139A ILE* 1.3 67.4 + - - +
1140A HIS* 3.4 18.3 + - + +
1149A ALA* 5.8 0.9 - - - -
1152A TYR* 3.4 45.9 - + + -
1165A VAL* 5.3 1.6 - - + -
1166A VAL 2.7 15.4 + - - +
1167A THR* 4.3 15.0 - - + -
1168A ILE* 3.2 29.9 + - - +
1218A PHE* 3.2 59.6 - + + -
1219A GLY* 3.4 12.3 - - - -
1220A GLU* 3.3 35.2 - - + -
1246A GLU* 3.6 11.2 - - - -
1472A LEU* 3.4 25.4 - - + -
1475A VAL* 5.3 0.2 - - + -
1476A PHE* 3.4 18.2 - + + -
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Residues in contact with ILE1139 (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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1137A VAL* 4.5 5.6 - - + +
1138A TRP* 1.3 79.0 - - - +
1140A HIS* 1.3 66.3 + - - +
1168A ILE* 3.7 23.3 - - + -
1170A TYR* 3.8 13.7 - - + -
1194A GLN* 3.7 31.0 - - + +
1198A LEU* 6.3 0.9 - - + -
1217A ILE* 5.1 7.9 - - + -
1218A PHE 3.0 14.2 + - - +
1219A GLY* 3.3 18.4 - - - -
1220A GLU 3.6 1.7 + - - -
1223A GLY* 3.3 19.4 - - - +
1226A SER* 4.1 4.7 - - - -
1227A VAL* 4.2 14.8 - - + -
1230A LEU* 4.0 26.5 - - + -
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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