Contacts of the helix formed by residues 635 - 643 (chain E) in PDB entry 1FSJ
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 635 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616E LYS 3.3 7.6 - - - +
618E VAL* 3.8 21.8 - - + -
622E TRP* 3.6 38.1 - - + -
633E PRO 3.5 5.4 - - - +
634E ILE* 1.4 91.9 - - + +
636E ASP* 1.3 67.7 - - - +
637E ARG* 4.4 4.7 - - + +
638E ILE* 3.0 31.9 + - + +
639E ALA* 3.0 10.0 + - - +
657E VAL* 6.1 1.3 - - + -
661E VAL* 5.9 0.2 - - + -
667E LEU* 4.0 16.8 - - + -
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Residues in contact with ASP 636 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614E LYS* 3.4 21.7 - - - +
615E GLY 4.5 1.1 - - - +
616E LYS 2.8 22.2 + - - +
617E PRO* 3.3 32.3 - - + +
618E VAL* 5.3 0.9 + - - +
634E ILE 3.5 0.6 + - - -
635E PRO* 1.3 73.6 - - - +
637E ARG* 1.3 89.6 + - - +
639E ALA* 3.3 2.1 + - - +
640E ASP* 3.0 39.0 + - - +
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Residues in contact with ARG 637 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618E VAL* 5.0 12.1 + - - +
635E PRO* 3.1 2.5 - - + -
636E ASP* 1.3 92.2 + - - +
638E ILE* 1.3 66.7 + - + +
640E ASP* 3.5 10.7 + - - +
641E LYS* 3.4 25.8 + - - +
664E ASP* 2.8 46.2 + - - +
666E GLU* 3.5 21.8 - - - +
667E LEU* 3.7 22.2 - - + +
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Residues in contact with ILE 638 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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634E ILE* 4.2 14.6 - - + -
635E PRO* 3.0 20.1 + - + +
637E ARG* 1.3 81.1 - - - +
639E ALA* 1.3 61.6 + - - +
641E LYS* 3.1 16.5 + - + +
642E LEU* 3.2 33.9 + - + +
657E VAL* 4.5 14.6 - - + -
660E GLU* 3.6 39.0 - - + +
661E VAL* 3.7 10.5 - - + +
664E ASP* 5.1 2.2 - - + +
667E LEU* 3.6 31.4 - - + -
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Residues in contact with ALA 639 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614E LYS 3.0 37.0 - - - +
615E GLY* 4.0 3.8 - - - +
634E ILE* 4.3 3.5 - - + +
635E PRO 3.0 11.0 + - - +
636E ASP 3.3 3.8 + - - +
638E ILE* 1.3 77.1 - - - +
640E ASP* 1.3 56.6 + - - +
643E ARG* 3.0 40.8 + - - +
716E MET* 3.3 25.9 - - + +
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Residues in contact with ASP 640 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614E LYS 5.0 0.5 - - - +
636E ASP* 3.0 25.9 + - - +
637E ARG* 3.7 11.1 - - - +
638E ILE 3.2 0.2 - - - -
639E ALA* 1.3 77.2 - - - +
641E LYS* 1.3 64.7 + - + +
643E ARG* 3.0 42.0 + - - +
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Residues in contact with LYS 641 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637E ARG 3.4 13.4 + - - +
638E ILE* 3.1 11.5 + - + +
640E ASP* 1.3 81.8 - - + +
642E LEU* 1.3 60.4 + - - +
643E ARG 3.5 1.3 - - - +
645E LYS* 3.5 17.2 - - - +
660E GLU* 3.8 42.0 + - + +
663E LYS* 6.1 2.3 - - - +
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Residues in contact with LEU 642 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611E ALA* 3.3 14.5 - - + +
638E ILE* 3.2 26.8 + - + +
641E LYS* 1.3 79.5 - - - +
643E ARG* 1.3 69.7 + - - +
645E LYS* 3.1 35.9 + - - +
647E PHE* 4.0 6.3 - - + -
653E PHE* 3.9 11.7 - - + -
656E ALA* 3.8 21.3 - - + +
657E VAL* 3.8 39.0 - - + +
660E GLU* 4.0 17.9 - - + +
716E MET* 4.1 13.2 - - - -
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Residues in contact with ARG 643 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611E ALA 3.8 9.2 - - - +
612E THR* 4.6 6.3 - - - -
613E GLY 3.0 29.9 + - - +
614E LYS* 3.7 14.9 + - - +
639E ALA* 3.0 25.3 + - - +
640E ASP* 3.0 42.5 + - - +
641E LYS 3.5 3.0 - - - +
642E LEU* 1.3 78.6 - - - +
644E ASP* 1.3 88.3 + - - +
645E LYS* 3.0 10.2 + - - +
716E MET* 3.9 5.1 - - + +
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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
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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