Contacts of the helix formed by residues 515 - 525 (chain A) in PDB entry 1Q6S
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 SER 515 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A GLN* 4.3 1.4 + - - -
510A ILE* 3.2 16.1 + - - +
513A SER* 2.7 27.3 + - - -
514A GLY* 1.3 74.7 - - - +
516A TRP* 1.3 64.4 + - - +
517A ALA 3.2 2.9 - - - +
518A ALA* 3.2 15.6 + - - +
519A ILE* 3.1 32.4 + - - +
1181B ASP* 6.0 2.7 - - - -
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Residues in contact with TRP 516 (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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507A PHE* 3.4 31.2 - + - -
510A ILE* 3.3 39.7 - - + +
511A ASP* 2.7 28.3 + - - +
514A GLY* 3.4 6.2 - - - -
515A SER* 1.3 77.2 - - - +
517A ALA* 1.3 56.9 + - - +
519A ILE* 3.3 8.2 + - + +
520A TYR* 2.8 29.8 + - - +
764A ALA* 4.1 15.9 - - + +
767A LEU* 4.4 14.5 - - + +
768A ARG* 3.5 37.1 - - + +
771A TYR* 3.5 54.5 - + + -
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Residues in contact with ALA 517 (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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514A GLY 4.9 4.0 + - - +
515A SER 3.2 0.6 - - - -
516A TRP* 1.3 76.5 - - - +
518A ALA* 1.3 56.1 + - - +
520A TYR* 3.2 1.0 + - - +
521A GLN* 2.7 42.3 + - + +
764A ALA* 3.7 18.5 - - + +
1181B ASP 4.2 6.7 - - - +
1182B PHE* 3.6 34.3 - - + +
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Residues in contact with ALA 518 (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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515A SER* 3.2 21.0 + - - +
517A ALA* 1.3 77.8 - - - +
519A ILE* 1.3 59.0 + - + +
522A ASP* 2.9 32.8 + - - +
1118B SER* 5.4 3.4 - - - -
1119B LEU* 3.8 29.2 - - + -
1181B ASP* 5.1 6.5 - - + +
1182B PHE* 4.1 14.5 - - + -
1301B 214 3.3 7.0 - - + -
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Residues in contact with ILE 519 (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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510A ILE* 3.6 41.3 - - + -
515A SER* 3.1 22.1 + - - +
516A TRP* 3.5 11.4 - - + +
518A ALA* 1.3 77.4 - - + +
520A TYR* 1.3 63.7 + - - +
522A ASP* 3.3 7.8 + - - +
523A ILE* 3.1 27.9 + - + +
747A LYS* 3.7 39.3 - - + +
767A LEU* 3.8 15.7 - - + -
771A TYR* 4.8 2.2 - - - +
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Residues in contact with TYR 520 (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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516A TRP 2.8 17.5 + - - +
517A ALA 3.5 3.1 - - - +
519A ILE* 1.3 79.0 - - - +
521A GLN* 1.3 80.1 + - - +
523A ILE* 3.1 8.5 + - + +
524A ARG* 2.9 45.1 + - + +
750A LEU* 5.0 7.4 - - + -
754A ARG* 3.6 12.0 + - - -
760A LEU 5.0 0.2 - - - -
761A ILE* 2.6 41.6 + - + -
762A GLN* 3.0 24.8 + - - -
763A THR* 3.9 13.9 - - - -
764A ALA* 3.7 23.3 - - + -
767A LEU* 4.0 20.6 - - + -
6000A MPD 5.1 2.3 + - - -
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Residues in contact with GLN 521 (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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517A ALA* 2.7 24.9 + - - +
520A TYR* 1.3 94.6 - - - +
522A ASP* 1.3 66.7 + - - +
524A ARG* 2.9 37.4 + - - +
525A HIS* 3.0 35.7 + - + +
764A ALA* 6.1 0.2 - - - +
6000A MPD 5.1 2.0 + - - -
1182B PHE* 3.6 44.4 - - + +
1262B GLN* 4.7 10.5 + - - +
1263B THR* 5.0 6.3 - - - +
1301B 214 4.0 7.6 - - + -
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Residues in contact with ASP 522 (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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518A ALA 2.9 20.0 + - - +
519A ILE* 3.5 6.9 - - - +
521A GLN* 1.3 77.0 - - - +
523A ILE* 1.3 67.3 + - - +
525A HIS 3.4 0.3 + - - -
526A GLU* 3.3 29.3 + - - +
747A LYS* 6.0 1.7 - - - +
4000A MG 4.0 17.7 - - - -
1118B SER* 5.9 2.5 - - - +
1301B 214 3.4 41.1 - - + -
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Residues in contact with ILE 523 (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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519A ILE* 3.1 16.6 + - + +
520A TYR* 3.1 9.4 + - + +
522A ASP* 1.3 77.3 - - - +
524A ARG* 1.3 68.2 + - - +
526A GLU* 3.1 3.2 + - - -
527A ALA* 3.0 21.1 + - - +
747A LYS* 4.0 39.0 - - + +
750A LEU* 4.0 36.1 - - + -
751A LEU* 3.8 27.0 - - + +
754A ARG* 4.5 11.9 - - - +
767A LEU* 4.0 18.8 - - + -
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Residues in contact with ARG 524 (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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520A TYR* 2.9 44.0 + - + +
521A GLN* 2.9 37.4 + - - +
523A ILE* 1.3 79.2 - - - +
525A HIS* 1.3 79.2 + - + +
526A GLU 3.2 2.9 + - - -
527A ALA* 3.2 16.1 + - - +
754A ARG* 3.8 15.9 - - - +
762A GLN* 5.7 0.7 - - - +
801A 214 2.7 55.3 + - - +
6000A MPD 3.1 40.5 + - - +
1020B TYR* 5.9 0.8 - - - -
1024B ARG* 4.3 11.5 - - - +
1262B GLN* 5.2 5.9 + - - -
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Residues in contact with HIS 525 (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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521A GLN* 3.0 29.4 + - - -
522A ASP 3.4 1.8 + - - -
523A ILE 3.3 0.2 - - - -
524A ARG* 1.3 101.2 + - - +
526A GLU* 1.3 59.0 + - - +
527A ALA 5.1 1.3 - - - +
801A 214 5.8 0.9 - - - -
1024B ARG* 5.7 5.2 - - - -
1047B ARG* 3.1 22.2 + - - -
1048B ASP* 4.0 7.6 + - - +
1262B GLN* 4.7 0.2 + - - -
1301B 214 3.3 91.6 - + + -
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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