Contacts of the helix formed by residues 877 - 888 (chain A) in PDB entry 5J3V
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 877 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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875A GLN 4.1 4.0 - - - +
876A PHE* 1.3 90.8 - - + +
878A LEU* 1.3 60.8 + - - +
879A PRO* 3.4 5.8 - - + -
880A LEU* 3.2 32.6 + - + -
881A LYS* 2.9 26.2 + - - +
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Residues in contact with LEU 878 (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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876A PHE 3.8 1.7 + - - -
877A PRO* 1.3 70.9 - - - +
879A PRO* 1.3 73.2 - - + +
881A LYS* 3.4 15.9 + - + +
882A GLU* 3.0 54.9 + - + +
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Residues in contact with PRO 879 (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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877A PRO* 3.6 6.7 - - + -
878A LEU* 1.3 96.5 - - + +
880A LEU* 1.3 75.4 + - + +
882A GLU* 4.0 4.6 - - + +
883A ARG* 3.3 34.6 + - - +
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Residues in contact with LEU 880 (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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837A ASP* 4.1 19.5 - - - +
840A ALA* 3.7 35.7 - - + +
841A SER* 5.6 0.9 - - - -
876A PHE* 4.5 11.2 - - + -
877A PRO* 3.2 40.3 + - + +
878A LEU 3.2 0.6 - - - -
879A PRO* 1.3 89.3 - - + +
881A LYS* 1.3 66.1 + - - +
883A ARG* 3.5 9.6 + - - +
884A LEU* 3.3 31.6 + - - +
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Residues in contact with LYS 881 (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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873A SER* 3.2 33.9 - - - +
874A ASP* 3.8 27.8 + - - +
876A PHE* 3.9 24.4 + - + +
877A PRO 2.9 16.4 + - - +
878A LEU* 3.9 14.1 - - + +
880A LEU* 1.3 79.2 - - - +
882A GLU* 1.3 70.9 + - - +
884A LEU* 3.6 6.3 + - - +
885A ALA* 3.4 21.1 + - - +
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Residues in contact with GLU 882 (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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878A LEU* 3.0 44.9 + - + +
879A PRO* 4.3 4.7 - - + +
881A LYS* 1.3 82.7 - - + +
883A ARG* 1.3 65.3 + - - +
885A ALA* 3.5 7.9 + - - +
886A ALA* 3.1 26.0 + - - +
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Residues in contact with ARG 883 (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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840A ALA* 3.0 35.5 + - + +
841A SER 5.6 0.9 - - - -
842A TRP 3.9 19.9 + - - -
843A ILE* 4.2 21.3 + - - +
879A PRO* 3.3 27.1 + - - +
880A LEU* 3.9 10.7 - - - +
881A LYS 3.3 0.4 - - - -
882A GLU* 1.3 76.9 - - - +
884A LEU* 1.3 60.2 + - - +
886A ALA* 4.1 3.1 - - - +
887A PHE* 2.9 50.9 + - + +
888A TYR* 5.2 1.3 - - + -
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Residues in contact with LEU 884 (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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836A CYS* 4.1 34.5 - - + +
839A VAL* 4.6 1.1 - - + -
840A ALA* 3.8 24.0 - - + +
857A LEU* 4.0 17.1 - - + +
869A TRP* 5.0 17.9 - - + -
873A SER* 6.6 0.4 - - - -
876A PHE* 4.1 18.6 - - + -
880A LEU 3.3 17.1 + - - +
881A LYS* 4.0 5.8 - - - +
882A GLU 3.4 0.2 - - - -
883A ARG* 1.3 78.8 - - - +
885A ALA* 1.3 58.3 + - - +
888A TYR* 3.2 53.7 + - + +
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Residues in contact with ALA 885 (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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881A LYS* 3.4 15.4 + - + +
882A GLU* 3.9 9.6 - - - +
883A ARG 3.2 0.8 - - - -
884A LEU* 1.3 79.7 - - - +
886A ALA* 1.3 59.6 + - - +
888A TYR 3.0 16.5 - - - +
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Residues in contact with ALA 886 (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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850A ARG* 5.1 2.6 + - - -
882A GLU 3.1 18.0 + - - +
883A ARG* 4.1 3.8 - - - +
885A ALA* 1.3 77.2 - - - +
887A PHE* 1.3 62.6 + - + +
888A TYR 3.5 0.2 - - - -
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Residues in contact with PHE 887 (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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842A TRP 4.5 4.7 - - - -
843A ILE 3.5 27.4 - - - -
844A ASN* 5.3 2.9 - - - -
845A PRO* 4.1 18.4 - - + -
850A ARG* 3.3 60.2 + - - -
883A ARG* 2.9 34.9 + - + +
886A ALA* 1.3 80.1 - - - +
888A TYR* 1.3 91.0 + + + +
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Residues in contact with TYR 888 (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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839A VAL* 3.4 36.5 + - + +
840A ALA* 5.7 1.1 - - - -
842A TRP* 4.9 0.9 - - - +
845A PRO* 4.5 5.9 - - - +
850A ARG* 3.9 21.5 - - + -
853A PHE* 3.9 22.6 - + + -
854A CYS* 3.9 36.6 - - + -
857A LEU* 3.6 22.9 - - + -
858A HIS* 3.6 28.5 - - + +
883A ARG* 4.6 1.6 - - + -
884A LEU* 3.2 34.4 + - + +
885A ALA* 3.0 21.7 - - - +
886A ALA 5.1 0.2 - - - -
887A PHE* 1.3 114.8 - + + +
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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