Contacts of the helix formed by residues 703 - 719 (chain A) in PDB entry 4RIB
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 SER 703 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671A SER* 5.2 1.1 - - - -
700A CYS* 3.3 20.2 + - - +
701A PRO 3.0 1.2 - - - -
702A ASP* 1.3 86.9 + - - +
704A ARG* 1.3 58.2 + - - +
705A GLY 3.3 1.6 - - - -
706A ARG* 3.2 11.0 + - - +
707A TRP* 3.0 51.5 + - - -
952A ARG* 4.5 3.7 + - - +
0U T 4.4 17.8 - - - -
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Residues in contact with ARG 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A LEU* 2.1 49.9 + - + +
696A GLN* 3.3 16.4 + - - +
697A ARG* 3.1 30.6 - - - +
699A TYR 5.7 0.4 + - - -
700A CYS 4.0 3.6 - - - +
701A PRO* 2.7 39.9 + - + +
703A SER* 1.3 74.7 - - - +
705A GLY* 1.3 69.7 + - - +
707A TRP* 3.9 16.8 - - + -
708A TRP* 2.9 46.6 + - + +
735A ASP* 2.4 34.3 + - - +
737A GLU* 3.9 21.3 - - + -
738A VAL* 4.9 0.7 - - + -
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Residues in contact with GLY 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
701A PRO 4.6 0.6 + - - -
702A ASP 4.1 6.7 + - - -
703A SER 3.3 0.8 - - - -
704A ARG* 1.3 80.3 - - - +
706A ARG* 1.3 61.1 + - - +
708A TRP* 3.7 2.1 - - - +
709A ASP* 3.2 21.8 + - - +
737A GLU 4.9 1.0 + - - -
738A VAL* 3.9 30.6 - - - +
739A ARG 5.3 0.7 - - - -
742A HIS* 3.7 20.5 + - - +
746A LEU* 5.6 1.0 - - - +
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Residues in contact with ARG 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A ASP 4.9 1.2 + - - -
703A SER* 3.2 11.9 + - - +
704A ARG 3.2 0.4 - - - -
705A GLY* 1.3 73.9 - - - +
707A TRP* 1.3 69.4 + - + +
709A ASP* 3.5 4.2 + - - +
710A ARG* 3.0 35.0 + - + +
742A HIS* 3.4 34.6 + - + +
0U T 3.2 114.8 + - + +
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Residues in contact with TRP 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667A THR* 3.9 24.2 - - + -
668A ARG* 6.4 0.2 - - - -
671A SER* 2.8 29.6 + - - -
674A VAL* 6.0 1.1 - - + -
690A LEU* 3.6 26.1 - - + +
693A LEU* 3.7 47.2 - - + +
694A LEU* 3.8 24.0 - - + -
696A GLN* 4.0 6.1 - - - -
699A TYR 4.1 2.5 - - - -
700A CYS* 3.6 24.7 - - + -
703A SER* 3.0 29.5 + - - -
704A ARG* 3.0 24.0 + - + +
706A ARG* 1.3 84.9 - - + +
708A TRP* 1.3 52.9 + - - +
710A ARG* 3.1 5.2 + - + +
711A LEU* 2.8 34.8 + - - +
0U T 4.2 6.3 + - - -
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Residues in contact with TRP 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A LEU* 3.5 35.4 - - + +
697A ARG* 5.8 0.9 - - - -
704A ARG* 2.9 32.6 + - - +
705A GLY* 3.7 2.9 - - - +
707A TRP* 1.3 75.9 - - - +
709A ASP* 1.3 54.8 + - - +
711A LEU* 2.9 24.2 + - + +
712A ALA* 2.7 35.6 + - - +
728A CYS* 3.6 31.3 - - - -
731A GLU* 3.6 33.4 - - + -
732A GLY* 3.6 18.1 - - - -
735A ASP* 3.2 21.3 + - + -
738A VAL* 3.6 19.7 - - + -
746A LEU* 4.4 15.5 - - + -
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Residues in contact with ASP 709 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705A GLY 3.2 15.5 + - - +
706A ARG* 3.5 7.9 - - - +
708A TRP* 1.3 79.0 - - - +
710A ARG* 1.3 57.4 + - - +
712A ALA* 3.3 7.3 - - - +
713A LEU* 3.0 28.1 + - - +
742A HIS* 2.8 34.2 + - + +
745A SER* 2.9 39.4 + - - +
746A LEU* 4.3 10.1 + - + +
749A ARG* 4.9 7.4 + - - -
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Residues in contact with ARG 710 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
674A VAL* 5.3 1.1 - - + -
678A GLN* 2.6 41.9 + - - +
683A TYR* 4.8 1.2 - - - -
690A LEU* 4.0 10.8 - - + -
706A ARG* 3.0 25.7 + - - +
707A TRP* 3.1 6.7 + - + +
709A ASP* 1.3 76.5 - - - +
711A LEU* 1.3 66.3 + - - +
713A LEU* 3.5 21.0 + - - +
714A ASN* 3.0 49.3 + - - +
0U T 3.7 27.7 + - + +
5W G 2.9 44.2 + - - -
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Residues in contact with LEU 711 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A VAL* 3.6 35.2 - - + +
690A LEU* 3.7 16.5 - - + +
691A GLU* 4.2 17.9 - - + -
694A LEU* 3.7 24.2 - - + -
707A TRP 2.8 13.4 + - - +
708A TRP* 3.3 15.5 - - + +
710A ARG* 1.3 74.5 - - - +
712A ALA* 1.3 68.8 + - - +
714A ASN* 3.2 4.3 + - - +
715A LEU* 3.0 37.1 + - + +
728A CYS* 3.8 21.5 - - + -
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Residues in contact with ALA 712 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
708A TRP 2.7 15.5 + - - +
709A ASP 3.3 11.0 - - - +
711A LEU* 1.3 73.6 - - - +
713A LEU* 1.3 67.7 + - - +
715A LEU* 3.3 3.1 + - - +
716A HIS* 3.0 23.5 + - - +
725A THR* 4.3 4.1 + - + -
728A CYS* 3.5 20.2 - - - -
729A ILE* 4.7 4.9 - - + -
746A LEU* 4.1 17.3 - - + -
749A ARG* 4.1 17.9 - - - +
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Residues in contact with LEU 713 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A ASP 3.0 13.9 + - - +
710A ARG* 3.5 29.8 - - - +
712A ALA* 1.3 77.7 - - - +
714A ASN* 1.3 63.5 + - - +
716A HIS* 3.6 0.5 - - - +
717A GLN* 2.6 41.1 + - + +
718A HIS* 3.6 29.8 - - + +
749A ARG* 3.6 27.2 - - - +
4W C 3.7 32.3 - - - +
5W G 3.8 9.9 - - - +
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Residues in contact with ASN 714 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678A GLN* 3.1 24.2 + - - +
683A TYR* 3.5 24.5 - - + -
686A ALA* 4.7 5.3 - - - +
687A VAL* 3.9 16.3 - - + +
690A LEU* 3.6 17.8 - - - +
710A ARG* 3.0 39.5 + - - +
711A LEU 3.2 3.1 + - - +
713A LEU* 1.3 83.0 - - - +
715A LEU* 1.3 58.2 + - - +
718A HIS* 2.9 28.9 + - - +
719A LEU* 3.0 13.1 + - - +
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Residues in contact with LEU 715 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A VAL* 3.8 24.0 - - + -
711A LEU* 3.0 32.7 + - + +
712A ALA 3.7 0.7 - - - +
714A ASN* 1.3 74.2 - - - +
716A HIS* 1.3 60.8 + - - +
719A LEU* 3.2 17.9 - - + -
720A LYS 2.8 27.2 + - - -
721A ARG* 3.0 15.9 + - + +
724A PRO* 3.9 30.7 - - + -
725A THR* 3.5 17.0 - - - +
728A CYS* 4.1 20.0 - - + -
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Residues in contact with HIS 716 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712A ALA 3.0 14.8 + - - +
713A LEU 3.6 2.0 - - - +
715A LEU* 1.3 78.5 - - - +
717A GLN* 1.3 73.9 + - + +
720A LYS* 3.0 27.6 - - + +
721A ARG 4.3 3.1 - - - +
722A LEU* 4.1 19.8 - - + +
725A THR* 3.1 21.2 + - + +
749A ARG* 3.1 31.7 + - + +
752A ARG* 4.6 17.7 - - + -
753A LEU* 3.5 27.6 - - + +
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Residues in contact with GLN 717 (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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713A LEU* 2.6 21.7 + - + +
716A HIS* 1.3 93.1 + - + +
718A HIS* 1.3 74.7 + - + +
720A LYS* 3.3 33.6 + - - +
749A ARG* 4.2 3.1 - - - +
3W G 4.5 4.4 + - - -
4W C 3.2 43.4 + - - +
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Residues in contact with HIS 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681A HIS* 5.6 1.1 - + - -
683A TYR* 3.2 59.3 - + + -
713A LEU* 3.6 23.9 - - + +
714A ASN* 2.9 17.6 + - - +
717A GLN* 1.3 81.3 + - + +
719A LEU* 1.3 68.9 + - - +
720A LYS* 3.4 3.1 - - - +
4W C 3.7 4.3 + - - -
5W G 3.0 31.7 + - - -
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Residues in contact with LEU 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683A TYR* 4.2 17.9 - - + +
684A GLU* 4.0 33.9 - - + +
687A VAL* 3.6 32.5 - - + -
714A ASN 3.0 9.6 + - - +
715A LEU* 3.2 24.9 - - + +
718A HIS* 1.3 81.6 - - - +
720A LYS* 1.3 70.2 + - - +
721A ARG* 3.1 12.8 + - + +
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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
------------------------------------------------------------
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