Contacts of the helix formed by residues 685 - 697 (chain A) in PDB entry 3JUE
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 ASN 685 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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648A THR* 4.9 1.0 + - - +
651A GLY* 3.7 20.2 + - - -
653A THR* 4.5 2.8 + - - -
680A ALA* 3.0 10.6 + - - +
683A THR* 3.6 19.3 + - - +
684A ALA* 1.3 73.5 - - - +
686A ALA* 1.3 62.3 + - - +
687A ASP* 3.4 10.7 + - - +
688A ILE* 3.2 45.1 + - + +
689A VAL* 3.0 26.7 + - - +
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Residues in contact with ALA 686 (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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684A ALA 3.7 4.6 + - - +
685A ASN* 1.3 72.7 + - - +
687A ASP* 1.3 61.0 + - - +
689A VAL* 3.8 7.5 - - - +
690A THR* 2.8 35.9 + - - +
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Residues in contact with ASP 687 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A THR* 4.1 23.4 + - + +
685A ASN* 3.3 9.0 + - - +
686A ALA* 1.3 81.7 - - - +
688A ILE* 1.3 57.8 + - - +
690A THR* 3.2 7.6 + - - -
691A LEU* 2.9 30.1 + - - +
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Residues in contact with ILE 688 (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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644A LEU* 6.0 0.2 - - + -
647A ALA 4.2 0.7 - - - +
648A THR* 3.9 37.7 - - - +
651A GLY* 4.1 5.8 - - - -
652A HIS 4.2 1.6 - - - +
653A THR* 3.6 39.5 - - + +
656A ALA* 4.4 15.5 - - + -
680A ALA* 4.1 4.9 - - + -
685A ASN* 3.2 30.6 + - + +
687A ASP* 1.3 71.8 - - - +
689A VAL* 1.3 67.2 + - - +
691A LEU* 3.2 7.1 + - + +
692A LEU* 2.9 43.5 + - + +
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Residues in contact with VAL 689 (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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677A LEU* 3.9 18.8 - - + +
680A ALA* 3.4 32.0 - - + +
681A MET* 3.3 40.2 - - + +
685A ASN 3.0 19.8 + - - +
686A ALA* 3.8 7.2 - - - +
688A ILE* 1.3 75.9 - - - +
690A THR* 1.3 57.8 + - - +
692A LEU* 3.8 1.0 - - - +
693A ARG* 2.9 36.5 + - + +
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Residues in contact with THR 690 (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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686A ALA* 2.8 23.4 + - - +
687A ASP* 3.4 7.4 - - - -
689A VAL* 1.3 79.9 - - - +
691A LEU* 1.3 56.2 + - - +
693A ARG* 3.7 4.8 - - - +
694A LEU* 2.8 49.1 + - + +
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Residues in contact with LEU 691 (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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653A THR* 3.9 34.5 - - + +
656A ALA* 4.0 11.7 - - + -
657A CYS* 4.0 33.4 - - + +
660A LEU* 4.3 12.6 - - + +
687A ASP 2.9 15.5 + - - +
688A ILE* 3.4 13.2 - - + +
690A THR* 1.3 74.8 - - - +
692A LEU* 1.3 53.6 + - + +
694A LEU* 3.2 10.5 + - + +
695A ALA* 2.7 36.4 + - - +
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Residues in contact with LEU 692 (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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644A LEU* 4.4 9.4 - - + -
660A LEU* 3.9 23.3 - - + -
666A LEU* 3.5 33.3 - - + +
676A PRO* 3.4 24.5 - - + +
677A LEU* 3.4 42.4 - - + +
680A ALA* 4.1 3.4 - - + -
688A ILE* 2.9 36.2 + - + +
689A VAL 3.8 2.9 - - - +
691A LEU* 1.3 73.8 - - + +
693A ARG* 1.3 65.7 + - - +
695A ALA* 3.4 1.9 + - - -
696A LYS* 3.1 20.4 + - - +
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Residues in contact with ARG 693 (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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677A LEU* 4.2 27.3 - - - +
689A VAL* 2.9 23.2 + - + +
690A THR* 3.7 5.2 - - - +
692A LEU* 1.3 78.4 - - - +
694A LEU* 1.3 61.1 + - + +
696A LYS* 3.3 41.8 + - - +
697A MET* 3.3 12.0 + - - +
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Residues in contact with LEU 694 (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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690A THR* 2.8 37.1 + - + +
691A LEU* 3.5 10.1 - - + +
693A ARG* 1.3 77.9 - - - +
695A ALA* 1.3 60.7 + - - +
697A MET* 3.0 41.2 + - + +
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Residues in contact with ALA 695 (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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660A LEU* 3.9 26.9 - - + -
666A LEU* 3.5 18.5 - - + +
691A LEU 2.7 19.5 + - - +
692A LEU* 3.6 7.0 - - - +
694A LEU* 1.3 73.2 - - - +
696A LYS* 1.3 61.3 + - - +
697A MET 3.5 4.2 + - - -
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Residues in contact with LYS 696 (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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666A LEU* 3.5 23.5 - - + +
667A GLY* 6.0 3.4 - - - +
692A LEU 3.1 13.0 + - - +
693A ARG* 3.5 37.2 - - - +
694A LEU 3.2 0.4 - - - -
695A ALA* 1.3 77.8 - - - +
697A MET* 1.3 61.5 + - - +
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Residues in contact with MET 697 (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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693A ARG 3.3 8.3 + - - +
694A LEU* 3.0 36.1 + - - +
695A ALA 4.1 4.7 - - - -
696A LYS* 1.3 80.9 - - - +
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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