Contacts of the helix formed by residues 639 - 649 (chain B) in PDB entry 1J1C
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 VAL 639 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638B THR* 1.3 72.2 - - - +
640B TYR* 1.3 57.7 + - - +
642B VAL* 3.9 0.8 - - - +
643B ALA* 2.9 30.2 + - + +
661B TYR* 4.8 7.4 - - + -
684B PRO* 3.7 21.3 - - + +
687B LEU* 2.8 39.4 + - + +
689B LEU* 3.6 29.1 - - + +
696B LEU* 3.9 12.8 - - + -
746B VAL* 4.7 2.9 - - + -
750B LEU* 3.9 33.2 - - + -
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Residues in contact with TYR 640 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B THR* 3.0 7.1 - - - +
639B VAL* 1.3 79.1 - - - +
641B ARG* 1.3 71.9 + - + +
643B ALA* 4.0 2.9 - - - +
644B ARG* 3.1 59.8 + - + +
684B PRO* 3.1 30.2 + - + -
685B GLN* 3.4 50.7 + - + -
722B TYR* 6.0 0.7 - - - -
749B GLU* 5.9 2.0 - - - -
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Residues in contact with ARG 641 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
636B PRO 3.4 19.0 + - - -
637B GLU* 2.9 39.2 + - - +
638B THR* 3.1 22.1 + - - +
640B TYR* 1.3 83.4 - - + +
642B VAL* 1.3 67.9 + - - +
644B ARG* 3.2 31.7 + - - +
645B HIS* 3.0 38.5 + - + -
930B ADP 6.1 0.2 - - - -
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Residues in contact with VAL 642 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B GLU* 4.1 22.9 - - + +
638B THR 3.1 16.1 + - - +
639B VAL* 3.9 2.7 - - - +
641B ARG* 1.3 77.0 - - - +
643B ALA* 1.3 63.4 + - - +
645B HIS* 3.1 20.0 + - - +
646B TYR* 3.2 33.9 + - + -
653B LEU* 4.0 19.7 - - + -
661B TYR* 5.0 4.9 - - + +
689B LEU* 4.0 21.3 - - + -
691B PRO* 5.5 4.5 - - + -
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Residues in contact with ALA 643 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639B VAL* 2.9 20.2 + - + +
640B TYR* 4.0 4.3 - - - +
642B VAL* 1.3 78.8 - - - +
644B ARG* 1.3 57.1 + - - +
646B TYR* 3.4 7.8 + - - +
647B SER* 2.9 29.4 + - - -
653B LEU* 6.0 3.1 - - - -
684B PRO* 6.0 1.6 - - + -
749B GLU* 5.7 8.5 - - + +
750B LEU* 3.9 25.1 - - + -
753B GLY* 6.1 0.3 - - - -
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Residues in contact with ARG 644 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640B TYR* 3.1 49.7 + - + +
641B ARG* 3.4 35.4 + - - +
642B VAL 3.2 0.2 - - - -
643B ALA* 1.3 74.7 - - - +
645B HIS* 1.3 69.5 + - - +
647B SER* 3.6 8.0 - - - -
648B ARG* 2.9 74.1 + - + +
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Residues in contact with HIS 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637B GLU* 4.2 19.0 + - - -
641B ARG* 3.0 32.3 + - + -
642B VAL* 3.1 15.7 + - - +
644B ARG* 1.3 89.6 + - - +
646B TYR* 1.3 67.2 + - + +
648B ARG* 3.5 15.7 + - - +
649B ALA* 3.3 23.0 + - - +
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Residues in contact with TYR 646 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B VAL* 3.2 30.4 + - + -
643B ALA* 3.7 7.9 - - - +
645B HIS* 1.3 82.0 - - + +
647B SER* 1.3 61.6 + - - +
649B ALA* 3.4 3.1 + - - +
650B LYS 3.2 2.4 + - - -
651B GLN* 2.7 62.4 + - + +
652B THR 3.5 27.4 - - - -
653B LEU* 3.6 33.8 - - + +
654B PRO* 3.9 17.7 - - + +
657B TYR* 5.3 4.5 - - - -
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Residues in contact with SER 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B ALA 2.9 17.7 + - - -
644B ARG* 3.2 11.6 + - - -
646B TYR* 1.3 75.1 - - - +
648B ARG* 1.3 67.2 + - - +
650B LYS* 2.9 17.9 + - - +
651B GLN 4.2 4.7 - - - -
753B GLY* 2.7 32.7 + - - -
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Residues in contact with ARG 648 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B ARG* 2.9 64.2 + - + +
645B HIS* 3.8 14.3 - - - +
647B SER* 1.3 74.7 - - - +
649B ALA* 1.3 58.5 + - - +
650B LYS* 2.8 17.2 + - - +
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Residues in contact with ALA 649 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645B HIS 3.3 14.0 + - - +
646B TYR* 4.0 1.8 - - - +
647B SER 3.3 0.2 - - - -
648B ARG* 1.3 75.8 - - - +
650B LYS* 1.3 69.9 + - - +
651B GLN* 2.9 38.1 + - + +
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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