Contacts of the strand formed by residues 1269 - 1273 (chain F) in PDB entry 6X34
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 CYS1269 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1260F VAL* 2.8 48.1 + - + +
1267F PRO 3.7 4.4 + - - +
1268F PRO* 1.3 75.2 - - - +
1270F LEU* 1.3 69.7 + - - +
1271F ARG* 3.9 4.9 - - - +
1438F ARG* 5.9 4.3 - - - -
1563F GLN* 4.8 8.5 - - + -
1564F PHE* 3.2 23.3 - - - +
1565F GLU* 4.7 0.4 - - - +
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Residues in contact with LEU1270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257F VAL* 4.8 10.5 - - + +
1258F SER 3.6 6.3 - - - +
1259F ARG* 3.7 38.8 - - + +
1268F PRO* 6.5 0.7 - - + -
1269F CYS* 1.3 82.9 - - - +
1271F ARG* 1.3 63.7 + - - +
1272F LEU* 5.4 0.2 - - - +
1291F LEU* 5.0 9.6 - - + -
1562F ILE 3.9 1.4 - - - +
1563F GLN* 3.6 1.9 - - - -
1564F PHE* 3.2 59.8 + - + +
1595F LEU* 4.8 20.9 - - + +
1596F GLU* 5.5 0.2 - - - -
1597F MET* 5.2 8.3 - - + +
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Residues in contact with ARG1271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1257F VAL* 3.3 24.0 - - - +
1258F SER* 3.6 30.1 + - - +
1260F VAL* 3.9 23.2 - - + +
1269F CYS* 3.9 5.4 - - + +
1270F LEU* 1.3 75.2 - - - +
1272F LEU* 1.3 61.4 + - - +
1273F THR* 4.8 11.2 + - - +
1440F PHE* 4.3 28.2 - - + -
1560F ASN* 6.5 0.2 - - + -
1562F ILE 3.4 7.0 - - - +
1563F GLN* 3.8 17.5 - - + +
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Residues in contact with LEU1272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1254F HIS 5.8 0.2 - - - +
1255F TYR* 4.5 28.7 - - + -
1256F GLU 3.8 10.1 - - - +
1257F VAL* 5.4 6.5 - - + -
1270F LEU 5.4 0.4 - - - +
1271F ARG* 1.3 77.6 - - - +
1273F THR* 1.3 76.4 + - - +
1274F HIS* 4.6 6.3 - - + +
1289F LEU* 4.4 33.7 - - + -
1440F PHE* 5.7 0.2 - - - -
1556F PRO* 6.2 2.5 - - + -
1560F ASN* 3.6 7.6 - - - +
1561F VAL* 3.3 44.1 + - + +
1562F ILE 3.0 14.6 + - - +
1597F MET* 6.2 4.5 - - + -
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Residues in contact with THR1273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1255F TYR* 4.1 3.6 + - - -
1256F GLU* 3.1 41.2 + - - +
1258F SER* 5.9 2.8 + - - -
1271F ARG* 4.8 11.8 + - - +
1272F LEU* 1.3 82.7 + - - +
1274F HIS* 1.3 68.6 + - - +
1275F ARG* 4.3 0.9 + - + +
1559F GLN* 3.5 11.9 - - + +
1560F ASN* 5.5 1.8 - - + -
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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