Contacts of the helix formed by residues 1246 - 1261 (chain A) in PDB entry 5KHU
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 PRO1246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1245A VAL* 3.8 28.9 - - - -
1247A HIS* 3.8 28.9 - - - -
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Residues in contact with HIS1247 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1246A PRO* 3.8 27.1 - - - -
1248A ASN* 3.8 29.2 - - - +
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Residues in contact with ASN1248 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1247A HIS* 3.8 25.6 - - - +
1249A VAL* 3.7 30.1 - - - +
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Residues in contact with VAL1249 (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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1248A ASN* 3.7 29.4 - - - +
1250A GLN* 3.7 29.2 - - - +
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Residues in contact with GLN1250 (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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1249A VAL* 3.7 25.1 - - - +
1251A VAL* 3.7 29.6 - - - +
1253A ALA* 4.4 18.4 - - - +
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Residues in contact with VAL1251 (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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1250A GLN* 3.7 25.1 - - - +
1252A ALA* 3.7 29.8 - - - +
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Residues in contact with ALA1252 (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 VAL* 3.7 29.6 - - - +
1253A ALA* 3.8 25.6 - - - +
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Residues in contact with ALA1253 (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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1250A GLN* 4.4 17.0 - - - +
1252A ALA* 3.8 26.5 - - - +
1254A VAL* 3.7 29.4 - - - +
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Residues in contact with VAL1254 (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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1253A ALA* 3.7 25.1 - - - +
1255A VAL* 3.7 29.8 - - - +
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Residues in contact with VAL1255 (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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1254A VAL* 3.7 29.8 - - - +
1256A GLY* 3.7 26.7 - - - +
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Residues in contact with GLY1256 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1213A SER* 4.5 20.2 - - - +
1255A VAL* 3.7 26.2 - - - +
1257A ILE* 3.7 30.3 - - - +
1259A LEU* 4.3 19.3 - - - +
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Residues in contact with ILE1257 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1256A GLY* 3.7 26.5 - - - +
1258A GLY* 3.7 29.4 - - - +
1260A VAL* 4.6 12.3 - - - +
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Residues in contact with GLY1258 (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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1257A ILE* 3.7 29.4 - - - +
1259A LEU* 3.7 26.5 - - - +
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Residues in contact with LEU1259 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1256A GLY* 4.3 16.6 - - - +
1258A GLY* 3.7 29.8 - - - +
1260A VAL* 3.8 23.6 - - - +
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Residues in contact with VAL1260 (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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1257A ILE* 4.6 16.6 - - - +
1259A LEU* 3.8 27.6 - - - +
1261A TYR* 3.7 29.4 - - - +
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Residues in contact with TYR1261 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1218A GLY* 4.7 7.0 - - - +
1260A VAL* 3.7 29.2 - - - +
1262A GLN* 3.8 28.0 - - - +
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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