Contacts of the helix formed by residues 695 - 699 (chain B) in PDB entry 2JA7
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 ALA 695 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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779A PHE* 4.4 2.0 - - + -
400B HIS* 4.1 11.2 - - + -
401B PHE* 4.1 5.8 - - + +
402B GLY* 3.5 28.5 - - - +
517B THR* 4.5 11.7 - - - +
521B LEU* 4.1 20.3 - - + +
633B VAL 3.6 4.6 + - - +
694B ASP* 1.3 73.8 + - - +
696B GLU* 1.3 68.7 + - - +
698B GLU* 3.1 26.2 - - - +
699B GLU* 3.4 4.2 + - - +
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Residues in contact with GLU 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ILE* 6.1 0.2 - - - +
400B HIS* 4.5 8.6 + - - -
402B GLY* 3.7 16.0 - - - +
403B LYS* 3.7 34.9 - - - +
616B ILE* 4.0 22.2 - - + +
625B LYS* 5.6 6.1 - - + -
627B PHE* 4.0 27.7 - - + -
694B ASP* 3.5 14.8 + - - +
695B ALA* 1.3 78.6 - - - +
697B GLU* 1.3 61.7 + - - +
699B GLU* 3.1 32.4 - - - +
700B SER 4.4 0.2 + - - -
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Residues in contact with GLU 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B ARG* 5.3 8.6 + - - +
604B ARG* 3.2 10.0 + - - -
614B SER* 3.2 11.4 - - - -
615B MET* 2.9 48.4 + - - +
616B ILE* 3.3 14.8 - - + +
691B GLU* 3.5 21.1 - - - +
692B TYR 4.9 1.9 - - - +
693B ILE* 4.3 18.4 - - + +
694B ASP* 3.6 14.4 + - - +
695B ALA 3.4 0.4 - - - -
696B GLU* 1.3 77.2 - - - +
698B GLU* 1.3 68.1 + - - +
700B SER* 2.9 23.5 + - - +
701B ILE* 3.2 16.0 - - + +
740B HIS* 5.9 1.0 + - - -
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Residues in contact with GLU 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A PHE* 3.3 23.9 - - + -
782A ARG* 3.7 4.3 + - - -
785A PRO* 3.8 27.1 - - + +
517B THR 4.5 3.8 - - - +
519B TRP* 4.2 11.4 - - - +
521B LEU* 5.5 1.9 - - - +
635B ARG* 3.0 38.0 + - - -
637B LEU* 5.3 0.2 - - - +
693B ILE* 3.6 14.0 - - + +
694B ASP 3.2 16.2 + - - +
695B ALA* 3.1 22.9 + - - +
697B GLU* 1.3 74.7 - - - +
699B GLU* 1.3 63.3 + - - +
700B SER 2.9 1.4 + - - -
701B ILE* 3.0 22.6 + - - +
703B ILE* 4.1 8.9 - - + +
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Residues in contact with GLU 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
779A PHE* 3.2 22.0 - - + +
780A VAL* 2.9 54.8 + - + +
782A ARG* 2.3 30.1 + - - +
789A LYS* 4.9 4.2 - - - -
400B HIS* 2.8 38.9 + - + +
616B ILE* 5.8 2.0 - - + -
695B ALA 3.4 0.2 + - - -
696B GLU* 3.1 24.2 + - - +
698B GLU* 1.3 79.0 - - - +
700B SER* 1.3 55.5 + - - +
67I THR* 3.8 2.4 - - - +
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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
------------------------------------------------------------
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