Contacts of the strand formed by residues 1309 - 1313 (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 MET1309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1109A TYR* 5.5 0.2 - - - +
1113A SER* 2.7 38.8 - - - +
1114A ALA* 3.3 34.3 - - + +
1116A ASN* 4.7 13.2 - - + +
1308A TYR* 1.3 80.3 - - - +
1310A HIS* 1.3 55.9 + - - +
1311A LEU* 2.6 33.9 - - + +
1336A LEU* 5.4 0.2 - - - -
1337A GLU* 3.4 32.9 + - + +
1338A THR 5.5 0.7 - - - -
1339A ASP* 5.2 8.3 - - + -
252U LYS* 3.8 24.2 - - + +
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Residues in contact with HIS1310 (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* 5.0 1.1 - - + -
1154A ALA* 3.3 34.0 + - + +
1158A LEU* 4.1 20.3 - - + +
1308A TYR* 4.4 5.6 - - + -
1309A MET* 1.3 71.2 - - - +
1311A LEU* 1.3 72.9 + - - +
1312A PRO* 4.5 0.5 - - - +
1334A TRP* 2.9 48.2 - + + +
1335A ILE 5.0 0.9 - - - -
1336A LEU* 3.5 28.3 - - + +
248U HIS 4.4 6.4 - - - +
249U GLN* 3.3 38.8 + - + +
252U LYS* 3.1 27.9 - - - +
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Residues in contact with LEU1311 (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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1111A GLY 4.0 10.8 - - - +
1112A VAL* 4.1 5.4 - - + -
1113A SER* 3.2 25.1 - - - +
1309A MET* 2.6 30.5 - - + +
1310A HIS* 1.3 75.6 - - - +
1312A PRO* 1.3 67.6 - - + +
1313A GLN* 3.8 25.0 + - - +
1334A TRP* 3.6 9.6 - - - -
1335A ILE* 3.1 41.7 + - + +
1337A GLU* 3.4 44.2 - - + +
252U LYS* 4.5 2.5 - - + -
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Residues in contact with PRO1312 (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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1112A VAL* 5.4 3.8 - - + +
1310A HIS 4.5 0.4 - - - +
1311A LEU* 1.3 84.6 - - + +
1313A GLN* 1.3 71.8 + - - +
1314A THR* 3.9 5.8 + - - +
1333A GLU 3.7 3.4 - - - +
1334A TRP* 3.1 28.7 - - + -
249U GLN 3.8 14.4 - - - +
250U MET 4.2 14.8 - - - +
251U ALA* 4.2 16.8 - - + -
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Residues in contact with GLN1313 (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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1111A GLY 6.0 0.2 - - - -
1112A VAL* 4.4 10.1 - - - +
1311A LEU* 3.9 23.2 - - - +
1312A PRO* 1.3 92.8 + - - +
1314A THR* 1.3 66.6 + - - +
1315A ASP* 5.8 3.2 - - - +
1316A ASN* 2.9 42.1 + - - +
1318A LYS* 5.1 4.4 - - + +
1332A GLN* 3.4 4.9 - - - -
1333A GLU* 3.0 30.5 + - + +
1335A ILE* 3.6 36.2 - - + +
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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