Contacts of the helix formed by residues 718 - 730 (chain B) in PDB entry 5IY8
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 718 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A TYR* 3.4 26.7 + - + +
839A HIS* 4.1 6.0 - - + -
716B HIS 4.1 1.2 + - - -
717B ASN* 1.3 72.1 + - - +
719B SER* 1.3 61.2 + - - +
720B PRO* 3.4 27.3 - - + +
721B ARG* 2.8 37.4 + - + +
722B ASN* 3.6 2.8 + - - -
974B SER 5.1 1.2 - - - +
975B ARG* 4.2 17.5 + - - +
976B MET* 3.3 37.3 + - + +
278U THR* 5.4 11.1 + - - -
279U ARG* 6.0 3.2 - - - +
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Residues in contact with SER 719 (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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836A PHE* 5.5 7.9 - - - -
839A HIS* 3.1 39.0 + - - -
840A ALA* 3.9 14.6 - - - -
843A GLY* 3.1 18.2 - - - -
512B ALA* 4.4 5.9 - - - +
717B ASN 3.2 3.2 + - - -
718B GLN* 1.3 73.6 - - - +
720B PRO* 1.3 70.3 - - - +
722B ASN* 3.2 24.4 + - - +
723B THR* 3.2 12.5 + - - -
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Residues in contact with PRO 720 (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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839A HIS* 5.0 1.3 - - + -
843A GLY* 4.4 12.3 - - - +
847A LEU* 4.6 20.6 - - + -
718B GLN* 3.5 32.1 - - + +
719B SER* 1.3 96.3 - - - +
721B ARG* 1.3 64.0 + - - +
723B THR* 3.1 19.4 + - - +
724B TYR* 3.1 29.9 + - + -
279U ARG* 6.5 1.8 - - + -
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Residues in contact with ARG 721 (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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717B ASN* 4.5 6.1 - - + -
718B GLN* 2.8 30.5 + - + +
720B PRO* 1.3 78.7 - - - +
722B ASN* 1.3 60.3 + - - +
724B TYR* 3.3 31.9 - - - +
725B GLN 3.2 20.8 + - - -
728B MET* 5.3 0.2 - - - +
939B HIS 2.7 31.6 - - - +
940B GLY* 2.8 31.3 + - - -
941B GLN* 4.0 4.8 - - - +
975B ARG* 3.8 38.9 + - - +
977B THR* 3.3 29.9 + - + +
279U ARG* 4.6 16.6 - - - +
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Residues in contact with ASN 722 (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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836A PHE* 4.2 10.6 - - + -
512B ALA* 4.3 11.6 - - + +
708B ALA* 5.9 0.5 - - - +
711B ILE* 3.3 18.2 - - + +
714B PRO* 3.0 31.5 + - + -
717B ASN* 2.9 46.6 + - - +
718B GLN 3.7 2.8 + - - -
719B SER* 3.4 11.5 - - - +
721B ARG* 1.3 75.3 - - - +
723B THR* 1.3 63.0 + - - +
724B TYR 3.3 0.2 - - - -
725B GLN* 3.7 8.4 + - - +
726B SER* 3.4 21.7 + - - -
939B HIS 5.0 0.7 - - - +
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Residues in contact with THR 723 (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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844A ARG* 5.2 2.4 + - - +
847A LEU* 3.6 31.6 - - + +
512B ALA* 3.6 18.3 - - - +
513B GLU 4.3 3.4 - - - +
514B THR* 3.8 36.4 - - + +
516B GLU* 5.9 3.1 - - + +
719B SER 3.2 14.2 + - - -
720B PRO* 3.1 7.8 + - - +
722B ASN* 1.3 74.9 - - - +
724B TYR* 1.3 68.4 + - + +
726B SER* 3.3 5.4 + - - -
727B ALA* 3.3 19.1 + - - +
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Residues in contact with TYR 724 (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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847A LEU* 3.4 29.1 - - + +
850A THR* 6.1 0.9 - - - +
516B GLU* 3.7 39.0 - - + +
720B PRO* 3.1 24.4 + - + -
721B ARG* 3.3 36.3 - - - +
723B THR* 1.3 80.3 - - + +
725B GLN* 1.3 65.0 + - - +
727B ALA* 3.4 5.4 + - - +
728B MET* 3.1 33.7 + - + +
940B GLY 4.2 12.3 - - - +
942B LYS* 6.2 3.1 - - - -
279U ARG* 4.8 20.3 + - - -
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Residues in contact with GLN 725 (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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707B CYS 5.3 5.1 + - - +
710B ILE* 4.8 12.7 - - - +
711B ILE* 4.5 16.4 - - + -
721B ARG 3.2 9.8 + - - +
722B ASN* 3.7 8.9 + - - +
723B THR 3.5 0.4 - - - -
724B TYR* 1.3 73.7 - - - +
726B SER* 1.3 59.7 + - - +
728B MET* 2.8 27.3 + - - +
729B GLY* 2.9 22.5 + - - -
937B SER 3.4 10.9 - - - +
938B ARG* 3.2 30.0 + - - +
939B HIS 4.2 1.1 - - - -
940B GLY* 3.6 17.8 - - - +
1049B GLN* 3.4 36.2 + - - +
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Residues in contact with SER 726 (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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512B ALA 3.3 17.7 + - - -
513B GLU* 3.6 30.3 - - - +
514B THR 5.0 0.4 - - - -
707B CYS* 3.8 14.7 + - - -
708B ALA* 3.9 15.4 + - - -
722B ASN 3.4 9.0 + - - -
723B THR 3.3 10.4 + - - -
724B TYR 3.3 0.8 - - - -
725B GLN* 1.3 79.1 - - - +
727B ALA* 1.3 59.6 + - - +
729B GLY* 4.3 1.1 + - - -
730B LYS* 3.0 27.4 - - - +
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Residues in contact with ALA 727 (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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514B THR 5.1 4.6 + - - +
515B PRO* 5.7 0.4 - - + -
516B GLU* 4.4 36.8 - - + +
723B THR 3.3 10.0 + - - +
724B TYR* 3.7 8.1 - - - +
725B GLN 3.2 0.4 - - - -
726B SER* 1.3 79.2 - - - +
728B MET* 1.3 62.7 + - + +
730B LYS* 3.4 31.8 + - - +
731B GLN* 3.8 11.5 + - - +
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Residues in contact with MET 728 (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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516B GLU* 6.1 0.4 - - - +
721B ARG* 5.3 0.2 - - - +
724B TYR* 3.1 21.2 + - + +
725B GLN* 2.8 25.5 + - - +
727B ALA* 1.3 70.2 - - + +
729B GLY* 1.3 60.3 + - - +
730B LYS 3.2 0.2 - - - -
731B GLN* 2.9 28.7 + - + +
732B ALA* 3.3 7.8 + - - +
936B ALA* 3.5 28.0 - - + -
937B SER 4.4 0.2 - - - +
940B GLY* 3.1 40.4 - - - +
942B LYS* 3.4 39.0 - - + +
1049B GLN* 4.6 3.4 - - - +
1051B LEU* 4.0 12.1 - - + +
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Residues in contact with GLY 729 (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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474B THR* 4.1 7.0 + - - +
476B ALA* 5.4 5.9 - - - +
707B CYS* 5.5 5.4 - - - -
725B GLN* 2.9 21.4 + - - +
726B SER* 4.3 2.2 + - - -
727B ALA 3.4 0.4 - - - -
728B MET* 1.3 76.7 - - - +
730B LYS* 1.3 56.7 - - - +
732B ALA* 3.0 23.9 + - - +
774B ALA* 5.7 1.0 - - - +
1049B GLN* 3.7 17.9 - - - -
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Residues in contact with LYS 730 (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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471B ASN* 4.9 4.0 + - - +
473B LEU* 3.2 16.9 - - - +
474B THR* 4.7 0.7 - - - -
476B ALA* 5.8 0.2 - - - -
477B SER* 3.3 33.9 + - - +
480B SER* 3.9 20.4 - - - +
484B ARG* 4.0 19.7 - - - +
513B GLU* 4.9 5.5 - - + +
514B THR 5.6 1.6 - - - -
515B PRO* 5.3 14.3 - - - +
707B CYS* 3.5 20.4 - - - -
726B SER 3.0 19.7 - - - +
727B ALA* 3.5 19.6 - - - +
728B MET 3.2 0.2 - - - -
729B GLY* 1.3 74.7 - - - +
731B GLN* 1.3 58.9 + - + +
732B ALA 3.4 0.7 - - - -
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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