Contacts of the helix formed by residues 760 - 767 (chain B) in PDB entry 3E7C
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 GLN 760 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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597B GLN* 3.5 44.1 + - + +
598B TYR* 3.8 14.7 - - - -
600B TRP* 4.9 3.4 - - - +
737B PHE* 4.0 9.9 - - + -
756B ILE* 2.9 27.1 - - + +
757B ILE* 3.0 4.5 + - - +
758B THR 2.9 1.0 - - - -
759B ASN* 1.3 82.9 + - + +
761B ILE* 1.3 67.9 + - - +
762B PRO* 3.0 4.8 - - - -
763B LYS* 3.0 35.1 + - - +
764B TYR* 2.9 52.2 + - + +
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Residues in contact with ILE 761 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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737B PHE* 3.3 50.7 - - + -
740B PHE* 5.0 4.9 - - + -
741B LEU* 4.3 28.9 - - + -
757B ILE* 3.0 31.2 + - + +
758B THR* 3.9 10.5 - - + +
760B GLN* 1.3 72.1 - - - +
762B PRO* 1.3 70.0 - - + +
764B TYR* 3.3 11.6 + - - +
765B SER* 3.4 10.4 + - - -
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Residues in contact with PRO 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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758B THR 3.2 18.6 - - - +
759B ASN* 4.1 4.0 - - - +
760B GLN 3.3 4.7 - - - +
761B ILE* 1.3 93.6 - - + +
763B LYS* 1.3 55.4 + - + +
764B TYR 2.8 1.7 + - - -
765B SER* 2.8 31.7 + - - -
766B ASN* 2.8 15.5 + - - +
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Residues in contact with LYS 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594B THR* 4.9 8.9 + - - +
597B GLN* 3.9 19.6 + - - -
598B TYR* 4.1 23.7 + - + +
759B ASN* 4.1 23.1 - - - +
760B GLN* 3.0 29.0 + - - +
762B PRO* 1.3 81.0 - - + +
764B TYR* 1.3 58.1 + - + +
766B ASN* 3.8 8.1 - - - -
767B GLY 2.9 19.9 + - - -
768B ASN* 3.5 15.5 + - + +
769B ILE* 3.5 20.3 - - + +
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Residues in contact with TYR 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597B GLN 4.9 1.6 + - - -
598B TYR* 4.3 13.3 + - - -
600B TRP* 5.5 1.2 + - - -
602B TYR* 5.8 0.9 - - - -
730B GLU* 5.9 8.5 - - + -
733B LEU* 3.0 34.9 - - + +
737B PHE* 3.8 16.9 - + + -
760B GLN* 2.9 59.4 + - + +
761B ILE* 3.5 6.5 - - - +
762B PRO 2.9 0.8 - - - -
763B LYS* 1.3 77.1 - - - +
765B SER* 1.3 67.1 + - - +
766B ASN 3.1 0.9 - - - -
767B GLY* 3.3 10.3 + - - +
769B ILE* 4.0 21.8 - - + -
771B LYS* 6.3 2.9 - - - -
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Residues in contact with SER 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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761B ILE 3.4 7.8 + - - -
762B PRO* 2.8 17.2 + - - -
764B TYR* 1.3 76.3 - - - +
766B ASN* 1.3 59.8 + - - -
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Residues in contact with ASN 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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762B PRO 2.8 13.8 + - - +
763B LYS* 4.0 8.5 - - - +
765B SER* 1.3 79.3 - - - +
767B GLY* 1.3 63.9 + - - +
768B ASN* 3.4 11.3 + - + +
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Residues in contact with GLY 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677B LYS* 5.0 3.5 - - - +
763B LYS 2.9 11.2 + - - -
764B TYR* 3.3 11.1 + - - -
765B SER 3.3 0.6 - - - -
766B ASN* 1.3 78.3 - - - +
768B ASN* 1.3 57.0 + - - +
769B ILE* 3.1 16.8 + - - +
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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