Contacts of the helix formed by residues 763 - 774 (chain B) in PDB entry 4V1M
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 763 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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760A GLN* 5.1 1.0 + - - -
804A TYR* 3.4 24.4 - - + +
816A HIS* 4.2 4.7 - - + +
762B ASN* 1.3 72.6 - - - +
764B SER* 1.3 68.3 + - - +
765B PRO* 3.3 15.1 - - + +
766B ARG* 3.0 37.0 + - + +
767B ASN* 3.7 2.8 + - - -
1019B SER 4.6 3.2 + - - +
1020B ARG* 2.9 27.5 - - - +
1021B MET* 3.3 35.6 + - + +
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Residues in contact with SER 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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816A HIS* 3.0 54.0 + - - -
817A ALA* 3.4 15.7 + - - +
820A GLY* 3.4 13.5 - - - -
525B ALA* 5.1 1.0 - - - +
762B ASN 3.4 3.5 + - - -
763B GLN* 1.3 68.6 - - - +
765B PRO* 1.4 67.2 - - - +
767B ASN* 3.4 23.2 + - - +
768B THR* 3.5 9.8 + - - -
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Residues in contact with PRO 765 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
816A HIS* 5.4 0.4 - - + -
820A GLY* 4.4 16.8 - - - +
824A LEU* 3.9 17.3 - - + -
763B GLN* 3.4 26.2 - - + +
764B SER* 1.4 90.9 - - - +
766B ARG* 1.3 54.6 + - - +
767B ASN 3.1 2.9 - - - -
768B THR* 2.8 12.6 + - - +
769B TYR* 2.7 58.8 + - + +
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Residues in contact with ARG 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 ASN* 4.7 9.4 - - + -
763B GLN* 3.0 33.9 + - + +
765B PRO* 1.3 75.4 - - - +
767B ASN* 1.4 55.2 + - - +
769B TYR* 3.2 41.0 + - - +
770B GLN* 3.1 22.7 + - - +
984B HIS 3.8 17.6 - - - +
985B GLY 2.7 38.6 + - - -
986B GLN* 4.8 0.2 - - - +
1020B ARG* 3.1 65.5 + - + +
1022B THR* 4.5 9.0 - - - -
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Residues in contact with ASN 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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813A PHE* 3.8 16.7 - - + -
525B ALA* 4.2 11.7 - - + -
756B ILE* 3.3 28.9 - - + +
759B PRO* 2.9 32.8 + - - +
762B ASN* 3.2 35.6 + - - +
763B GLN 3.7 1.0 + - - -
764B SER* 3.4 15.5 + - - +
765B PRO 3.1 0.8 - - - -
766B ARG* 1.4 73.9 - - - +
768B THR* 1.4 53.5 + - - +
770B GLN* 3.3 2.9 + - - -
771B SER* 2.7 35.0 + - - -
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Residues in contact with THR 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
821A ARG* 4.9 2.1 + - - -
824A LEU* 3.8 28.3 - - + +
524B PRO 4.4 2.6 + - - -
525B ALA* 3.1 35.6 + - - +
527B THR* 3.7 21.7 - - + +
528B PRO 5.3 2.0 - - - +
529B GLU* 5.6 2.0 - - + +
764B SER* 3.6 10.2 + - - -
765B PRO* 2.8 20.8 + - - +
767B ASN* 1.4 72.8 - - - +
769B TYR* 1.4 58.4 - - + +
771B SER* 2.9 25.6 - - - +
772B ALA* 4.0 3.1 - - - +
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Residues in contact with TYR 769 (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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824A LEU* 3.5 29.9 - - + +
827A THR* 5.7 3.5 - - - +
529B GLU* 3.7 38.3 + - + +
765B PRO* 2.7 34.9 + - + +
766B ARG* 3.2 40.2 - - - +
768B THR* 1.4 77.4 - - + +
770B GLN* 1.3 64.2 + - - +
772B ALA* 3.2 10.5 - - - +
773B MET* 3.1 27.3 + - + +
985B GLY* 4.0 11.0 - - - +
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Residues in contact with GLN 770 (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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752B ALA* 5.1 3.4 + - - +
755B ILE* 6.0 2.1 - - + +
756B ILE* 3.8 19.3 - - + +
766B ARG 3.1 12.0 + - - +
767B ASN* 3.3 7.8 + - - +
769B TYR* 1.3 74.5 - - - +
771B SER* 1.3 57.2 + - - +
772B ALA 2.9 7.4 + - - -
773B MET* 3.1 21.9 + - - +
774B GLY* 3.1 21.7 + - - +
981B ALA* 4.9 0.2 - - - +
982B SER 2.8 21.5 - - - +
983B ARG* 3.3 40.8 - - + +
984B HIS 3.8 0.2 + - - -
985B GLY 4.0 1.3 - - - +
1093B GLN* 3.0 22.8 + - - +
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Residues in contact with SER 771 (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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525B ALA* 3.8 4.2 - - - +
526B GLU* 3.7 34.2 + - - +
527B THR 4.4 4.7 + - - +
752B ALA* 3.6 28.9 - - - -
753B ALA* 4.0 10.8 - - - -
756B ILE* 4.2 2.1 - - - +
767B ASN 2.7 26.0 + - - -
768B THR* 2.9 21.2 + - - +
770B GLN* 1.3 71.7 - - - +
772B ALA* 1.3 57.9 + - - +
775B LYS* 4.2 8.4 + - - -
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Residues in contact with ALA 772 (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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527B THR 5.3 4.5 - - - +
528B PRO* 6.0 3.1 - - + -
529B GLU* 5.1 12.1 - - + +
768B THR 4.0 4.5 - - - +
769B TYR* 3.2 11.4 - - - +
770B GLN 2.9 1.6 + - - -
771B SER* 1.3 75.0 - - - +
773B MET* 1.3 66.8 + - + +
774B GLY 3.6 1.1 - - - +
775B LYS* 3.6 25.5 - - - +
776B GLN* 3.4 18.7 + - - +
9P G 4.4 10.6 + - - +
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Residues in contact with MET 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
769B TYR* 3.1 20.3 + - + +
770B GLN* 3.1 21.3 + - - +
772B ALA* 1.3 76.2 - - + +
774B GLY* 1.3 52.5 + - - +
775B LYS 3.0 4.5 - - - -
776B GLN* 2.7 38.9 + - - +
777B ALA 3.3 0.2 + - - -
979B LYS* 5.3 2.5 - - - -
981B ALA* 3.7 14.6 - - + -
985B GLY* 3.3 37.2 - - - +
987B LYS* 3.7 35.0 - - + -
1093B GLN* 5.0 1.3 - - - +
1095B LEU* 3.3 28.5 - - + +
9P G 5.7 0.7 - - - +
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Residues in contact with GLY 774 (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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487B THR* 3.4 18.9 - - - +
489B SER* 5.0 6.4 - - - -
752B ALA* 6.4 2.0 - - - -
755B ILE* 6.4 2.0 - - - -
770B GLN* 3.1 28.3 + - - +
773B MET* 1.3 75.9 - - - +
775B LYS* 1.4 59.3 + - - +
776B GLN 3.2 0.2 - - - -
777B ALA* 3.3 13.4 + - - +
819B ALA* 5.0 1.0 - - - +
1093B GLN* 3.9 16.0 + - - -
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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