Contacts of the helix formed by residues 1291 - 1298 (chain A) in PDB entry 5XA0
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 VAL1291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1251A ASN 4.9 2.2 - - - +
1252A GLN* 4.4 22.9 - - + -
1284A CYS* 4.8 0.7 - - - -
1289A GLU* 3.0 7.9 - - + -
1290A ARG* 1.3 76.6 - - - +
1292A VAL* 1.3 57.9 + - - +
1293A GLN 3.7 0.2 - - - -
1294A HIS* 3.8 7.6 + - - +
1295A PHE* 3.0 30.8 + - + +
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Residues in contact with VAL1292 (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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1251A ASN 5.0 2.2 + - - +
1284A CYS* 2.7 36.6 - - + +
1285A SER* 3.1 21.8 - - - +
1286A GLU* 3.3 8.7 - - + +
1289A GLU* 3.6 9.3 + - + +
1290A ARG 3.0 2.0 - - - -
1291A VAL* 1.3 75.4 - - - +
1293A GLN* 1.3 68.2 + - - +
1295A PHE 3.0 1.0 + - - -
1296A VAL* 2.9 16.6 + - - +
1344A PHE* 3.3 15.3 - - + -
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Residues in contact with GLN1293 (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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1290A ARG 4.0 6.7 + - - +
1291A VAL 3.7 0.2 - - - -
1292A VAL* 1.3 76.7 - - - +
1294A HIS* 1.3 57.8 + - - +
1296A VAL* 4.0 4.1 - - - +
1297A HIS* 2.9 30.0 + - - +
1344A PHE 3.3 23.7 + - - +
1345A TYR* 3.7 22.0 - - - +
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Residues in contact with HIS1294 (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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1290A ARG 4.8 2.3 + - - +
1291A VAL* 3.8 8.8 + - - +
1292A VAL 3.2 0.4 - - - -
1293A GLN* 1.3 79.0 - - - +
1295A PHE* 1.3 57.9 + - - +
1297A HIS 2.9 3.9 + - - -
1298A CYS* 2.1 56.4 + - + +
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Residues in contact with PHE1295 (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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1251A ASN 5.0 1.3 - - - +
1252A GLN* 6.0 2.9 - - - +
1255A LEU* 5.2 11.5 - - + +
1283A LEU* 4.3 11.3 - - - +
1284A CYS* 2.9 31.2 - - + +
1291A VAL* 3.0 15.1 + - + +
1292A VAL 3.0 2.8 + - - -
1294A HIS* 1.3 74.6 - - - +
1296A VAL* 1.3 57.4 + - - +
1298A CYS* 4.8 1.6 - - - -
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Residues in contact with VAL1296 (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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1280A ASN* 2.8 50.2 - - + +
1281A PHE* 3.8 9.0 - - - +
1283A LEU* 5.2 0.2 - - - -
1284A CYS 3.6 10.7 + - - +
1292A VAL 2.9 14.7 + - - +
1293A GLN* 4.2 3.6 - - - +
1295A PHE* 1.3 77.9 - - - +
1297A HIS* 1.3 61.3 + - + +
1298A CYS 4.0 0.2 - - - -
1344A PHE* 6.4 0.2 - - + -
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Residues in contact with HIS1297 (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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1293A GLN 2.9 18.2 + - - +
1294A HIS* 2.9 2.9 - - - -
1296A VAL* 1.3 78.4 - - + +
1298A CYS* 1.3 63.9 + - - +
1299A ILE 3.2 3.4 - - - +
1300A GLU* 4.0 21.9 + - + +
1301A THR* 4.1 7.4 + - - -
1304A ARG* 5.6 1.1 - - + -
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Residues in contact with CYS1298 (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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1294A HIS* 2.1 46.3 + - + +
1295A PHE* 4.8 1.6 - - - -
1296A VAL 4.0 0.2 - - - -
1297A HIS* 1.3 70.7 - - - +
1299A ILE* 1.3 63.2 + - - +
1301A THR* 4.3 8.8 + - - -
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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