Contacts of the strand formed by residues 1333 - 1338 (chain A) in PDB entry 5IY8
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 GLU1333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1142A PHE* 4.2 5.7 - - - +
1143A LEU 5.2 1.4 + - - +
1145A GLY* 5.8 0.7 - - - -
1148A ALA* 3.7 26.3 - - + +
1149A ARG* 5.7 0.9 - - - +
1312A PRO* 3.7 2.2 - - - +
1313A GLN* 3.0 33.4 + - + +
1314A THR* 4.7 0.2 + - - -
1318A LYS* 5.1 4.2 - - + +
1319A LYS* 2.7 55.5 + - + +
1331A LEU* 3.7 6.6 - - - +
1332A GLN* 1.3 79.2 - - - +
1334A TRP* 1.3 73.5 + - - +
1335A ILE* 3.8 17.9 + - + +
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Residues in contact with TRP1334 (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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1143A LEU* 4.1 12.4 + - + +
1147A SER 4.7 0.4 - - - +
1148A ALA* 3.1 34.7 + - - +
1149A ARG 4.7 2.4 + - - -
1150A ASP* 3.1 25.4 - - - +
1151A ALA* 3.3 33.8 - - + +
1154A ALA* 3.9 5.8 - - + -
1310A HIS* 2.9 37.7 - + + +
1311A LEU 3.6 1.8 - - - -
1312A PRO* 3.1 41.7 - - + -
1333A GLU* 1.3 78.1 - - - +
1335A ILE* 1.3 65.9 + - - +
246U ARG* 6.5 0.2 - - + -
249U GLN* 3.9 21.5 - - + -
250U MET* 5.4 9.0 - - + -
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Residues in contact with ILE1335 (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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1140A THR* 4.3 15.3 - - + -
1141A VAL 4.1 4.0 - - - +
1142A PHE* 3.6 41.5 - - + +
1143A LEU* 4.6 3.8 - - - +
1310A HIS* 4.1 0.7 - - - -
1311A LEU* 3.1 39.6 + - + +
1313A GLN* 3.6 34.3 - - + +
1316A ASN* 5.2 2.2 - - - +
1318A LYS* 5.6 1.6 - - + -
1333A GLU* 3.8 20.2 - - + +
1334A TRP* 1.3 80.5 - - - +
1336A LEU* 1.3 67.6 + - - +
1337A GLU* 5.0 7.6 - - + +
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Residues in contact with LEU1336 (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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1140A THR* 3.8 2.8 - - - +
1141A VAL* 2.8 48.8 + - + +
1143A LEU* 3.6 32.2 - - + +
1154A ALA 5.0 0.4 - - - +
1157A ILE* 4.4 5.4 - - + -
1158A LEU* 3.5 46.7 - - + +
1161A LEU* 4.4 18.6 - - + -
1308A TYR* 5.7 1.3 - - + -
1309A MET 4.9 0.7 - - - -
1310A HIS* 3.5 32.8 - - + +
1311A LEU* 4.9 0.4 - - - -
1335A ILE* 1.3 75.6 - - - +
1337A GLU* 1.3 60.5 + - - +
1338A THR* 4.2 6.5 + - + -
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Residues in contact with GLU1337 (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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1109A TYR* 3.9 15.9 + - - -
1111A GLY 4.6 0.2 - - - +
1113A SER* 3.9 7.3 + - - -
1116A ASN* 5.7 4.2 - - + +
1117A VAL* 5.9 3.7 - - - +
1138A SER* 5.0 5.4 - - - +
1139A LEU 3.9 6.7 - - - +
1140A THR* 4.3 21.8 + - + +
1308A TYR* 4.0 1.8 - - - +
1309A MET* 3.4 38.9 + - + +
1311A LEU* 3.4 42.2 - - + +
1335A ILE* 5.0 5.8 - - + +
1336A LEU* 1.3 72.3 - - - +
1338A THR* 1.3 66.5 + - - +
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Residues in contact with THR1338 (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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1116A ASN* 4.0 3.4 + - - -
1138A SER* 3.3 7.3 + - - -
1139A LEU* 2.9 63.7 + - + +
1141A VAL* 5.1 2.7 - - + -
1161A LEU* 3.8 25.8 - - + -
1304A ILE* 5.3 5.7 - - + +
1307A VAL* 3.5 27.8 - - + +
1308A TYR* 4.9 1.3 - - + +
1309A MET* 5.5 1.3 - - - -
1336A LEU* 4.9 7.0 - - + +
1337A GLU* 1.3 82.2 - - - +
1339A ASP* 1.3 61.2 + - - +
1340A GLY 4.1 4.9 + - - -
1346A VAL* 6.3 0.4 - - + -
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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