Contacts of the helix formed by residues 753 - 764 (chain B) in PDB entry 1JQI
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 PRO 753 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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665B CYS* 4.3 13.0 - - + -
751B GLU 4.6 1.3 - - - +
752B MET* 1.3 93.9 - - + +
754B ALA* 1.3 65.3 + - - +
755B GLU 3.3 3.1 - - - -
756B ARG* 3.0 41.5 + - + +
757B TYR* 3.1 44.2 + - + +
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Residues in contact with ALA 754 (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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665B CYS* 4.7 5.6 - - - -
736B SER 4.7 1.9 - - - +
739B ALA* 4.7 6.3 - - + -
740B ILE* 3.9 27.9 - - + +
743B LEU* 4.0 25.8 - - + -
747B GLY* 4.4 6.1 - - - +
752B MET* 3.4 2.3 - - + -
753B PRO* 1.3 80.8 - - - +
755B GLU* 1.3 61.8 + - - +
757B TYR* 3.2 17.1 + - + +
758B TYR* 3.1 21.5 + - - +
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Residues in contact with GLU 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 3.0 34.5 - - + +
740B ILE* 4.1 7.9 - - - -
747B GLY 3.7 18.1 + - - +
748B TYR 4.7 2.9 - - - +
749B VAL 3.9 24.5 - - - +
750B THR* 4.2 21.0 - - + +
752B MET 4.2 6.3 + - - +
754B ALA* 1.3 78.1 - - - +
756B ARG* 1.3 67.9 + - - +
758B TYR* 3.4 4.0 + - - +
759B ARG* 2.7 68.2 + - - +
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Residues in contact with ARG 756 (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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430B VAL 5.5 1.0 + - - -
433B ALA* 3.5 38.5 + - - +
434B ALA* 4.0 14.6 - - - +
437B ASP* 3.9 24.5 - - - +
484B GLY 4.3 6.3 + - - -
485B CYS* 4.9 6.7 - - - +
486B ALA 5.2 1.8 - - - +
753B PRO* 3.0 32.2 + - + +
755B GLU* 1.3 81.2 - - - +
757B TYR* 1.3 80.1 + - - +
759B ARG* 3.2 30.4 + - - +
760B ASP* 2.8 54.6 + - - +
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Residues in contact with TYR 757 (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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483B ARG 4.9 5.6 + - - -
658B ILE* 3.5 16.7 - - + +
661B ALA* 3.7 41.4 + - + +
662B SER* 3.4 31.4 - - - +
665B CYS* 4.2 8.2 - - + +
736B SER* 4.0 3.6 - - - -
739B ALA* 5.7 0.9 - - + -
753B PRO* 3.1 43.9 + - + +
754B ALA* 3.2 16.1 + - + +
756B ARG* 1.3 99.0 + - - +
758B TYR* 1.3 57.6 + - - +
760B ASP* 3.8 3.8 - - - -
761B ALA* 2.8 33.4 + - - +
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Residues in contact with TYR 758 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 4.2 13.5 - - + -
333A THR* 3.7 6.8 + - - +
358A TYR* 3.1 55.8 + + - -
359A ARG* 6.6 0.2 - - + -
362A ARG* 3.7 29.5 - - + +
733B THR* 4.1 7.2 + - + -
736B SER* 3.5 21.2 - - - +
737B HIS* 3.3 43.9 - + + -
740B ILE* 3.7 24.7 - - + -
754B ALA 3.1 6.1 + - - +
755B GLU 3.5 8.5 - - - +
757B TYR* 1.3 77.2 - - - +
759B ARG* 1.3 65.2 + - + +
761B ALA* 3.8 1.7 - - - +
762B ARG* 3.3 21.1 + - - +
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Residues in contact with ARG 759 (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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207A LEU* 3.6 21.5 - - + +
348A TYR* 2.9 20.9 + - - -
358A TYR* 5.9 0.9 - - + -
359A ARG* 4.7 3.1 - - + +
437B ASP* 3.0 39.3 + - - -
438B LYS* 6.1 0.8 - - - +
607B LEU* 3.0 57.9 + - + +
608B GLY* 4.3 2.4 - - - -
610B ARG* 3.4 15.8 - - - +
755B GLU* 2.7 46.5 + - - +
756B ARG* 3.2 22.5 + - - +
758B TYR* 1.3 77.9 - - + +
760B ASP* 1.3 63.6 + - - +
762B ARG* 3.4 13.9 + - - +
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Residues in contact with ASP 760 (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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348A TYR* 4.0 4.3 - - - -
437B ASP* 4.7 2.4 - - - +
486B ALA* 3.5 34.9 + - + +
487B SER 5.2 0.5 + - - -
608B GLY* 3.5 3.5 - - - -
609B ILE* 2.8 33.7 + - + +
658B ILE* 4.0 10.5 - - + +
756B ARG* 2.8 49.6 + - - +
757B TYR* 3.9 6.1 - - - +
759B ARG* 1.3 70.9 - - - +
761B ALA* 1.3 66.1 + - - +
763B ILE* 3.1 24.8 - - - +
764B THR* 4.1 0.5 + - - +
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Residues in contact with ALA 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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658B ILE* 4.0 14.5 - - + +
729B SER 4.6 0.5 - - - +
732B ALA* 3.5 38.6 - - + +
733B THR* 3.7 10.1 + - - +
736B SER* 3.7 6.7 - - - +
757B TYR 2.8 18.3 + - - +
758B TYR 3.8 3.1 - - - +
759B ARG 3.3 0.2 - - - -
760B ASP* 1.3 77.3 - - - +
762B ARG* 1.3 61.3 - - - +
764B THR* 2.7 26.8 + - - -
765B GLU 4.1 0.9 + - - -
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Residues in contact with ARG 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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337A HIS* 2.8 44.9 + - - -
340A ILE* 3.7 20.3 - - + +
341A GLN* 2.8 42.4 + - - +
348A TYR* 4.0 10.5 - - + -
358A TYR* 3.7 28.9 - - + +
607B LEU* 4.1 13.7 - - + -
733B THR* 3.9 6.2 + - - -
758B TYR 3.3 11.0 + - - +
759B ARG 3.5 12.3 - - - +
760B ASP 3.2 1.2 - - - -
761B ALA* 1.3 78.3 - - - +
763B ILE* 1.3 61.1 + - - +
764B THR 3.4 0.5 + - - -
765B GLU* 3.2 26.3 + - - +
766B ILE* 3.8 8.2 - - + +
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Residues in contact with ILE 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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348A TYR* 3.4 36.3 - - + +
609B ILE* 3.9 19.7 - - + -
654B GLN* 5.4 0.2 - - - +
760B ASP 3.1 18.9 + - - +
762B ARG* 1.3 78.9 - - - +
764B THR* 1.3 61.9 + - + +
766B ILE* 2.9 29.6 + - + +
767B TYR* 3.1 41.6 + - + +
799B FAD 3.3 42.6 - - + -
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Residues in contact with THR 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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651B ILE* 4.2 7.1 - - + +
654B GLN* 3.6 25.1 - - - +
655B ALA* 4.1 18.6 - - + +
658B ILE* 4.2 16.2 - - + -
725B LYS* 2.8 26.9 + - - -
729B SER* 3.2 34.3 + - - -
732B ALA* 4.4 1.1 - - + +
760B ASP 4.2 3.1 - - - +
761B ALA* 2.7 20.7 + - - +
763B ILE* 1.3 78.5 - - + +
765B GLU* 1.3 56.4 + - - +
766B ILE 3.2 0.9 - - - -
767B TYR* 3.9 7.9 - - - -
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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