Contacts of the helix formed by residues 936 - 955 (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 GLY 936 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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895A GLU* 5.6 2.5 - - - -
898A LEU* 3.9 5.6 - - - -
932A VAL 2.9 18.1 + - - -
933A SER 4.1 7.0 - - - -
934A CYS 3.5 0.6 - - - -
935A LEU* 1.3 84.2 - - - +
937A GLY* 1.3 68.5 + - - +
938A PRO* 3.0 7.2 - - - +
939A VAL 2.9 12.8 + - - -
940A LEU* 3.5 7.2 + - - +
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Residues in contact with GLY 937 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A ILE* 3.0 31.7 - - - +
891A HIS* 3.8 1.8 - - - -
893A ALA 4.7 7.2 + - - -
898A LEU* 3.4 16.4 - - - +
936A GLY* 1.3 65.8 - - - -
938A PRO* 1.4 61.4 - - - +
939A VAL 3.1 0.7 + - - -
940A LEU* 3.2 3.1 + - - +
941A SER* 2.8 34.5 + - - -
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Residues in contact with PRO 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A HIS* 3.3 45.7 - - + +
893A ALA 5.7 1.3 - - - +
936A GLY 3.2 9.2 - - - +
937A GLY* 1.4 84.1 - - - +
939A VAL* 1.3 55.9 + - + +
941A SER* 4.0 1.0 - - - -
942A GLY* 3.1 14.7 + - - -
997A LEU* 2.9 27.4 - - + +
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Residues in contact with VAL 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A PHE* 5.9 1.6 - - + -
935A LEU* 3.4 46.0 - - + +
936A GLY 2.9 3.0 + - - -
938A PRO* 1.3 76.9 - - + +
940A LEU* 1.3 69.9 + - + +
942A GLY* 3.1 3.3 + - - -
943A VAL* 3.0 32.1 + - + +
971A PHE* 4.7 5.4 - - + -
973A LEU* 6.2 0.7 - - + -
994A LEU* 5.5 6.1 - - + -
997A LEU* 3.6 35.7 - - + +
998A GLY 4.2 11.2 - - - +
999A ALA* 4.4 11.4 - - + -
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Residues in contact with LEU 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A PHE* 6.2 3.8 - - + -
841A LEU* 3.9 32.3 - - + -
845A LEU* 4.4 17.7 - - + -
890A ILE* 4.1 8.5 - - + -
898A LEU* 4.1 16.8 - - + -
932A VAL* 3.7 40.6 - - + +
935A LEU* 4.0 19.1 - - + -
936A GLY 3.5 4.4 + - - +
937A GLY 3.2 6.4 + - - +
939A VAL* 1.3 80.4 - - + +
941A SER* 1.3 66.3 + - - +
943A VAL* 3.1 8.3 + - + +
944A CYS* 2.9 30.6 + - - -
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Residues in contact with SER 941 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A LEU* 2.6 40.2 + - - +
890A ILE* 3.6 9.0 - - - +
891A HIS* 3.5 23.0 - - - +
937A GLY 2.8 20.6 + - - -
938A PRO 4.0 2.7 - - - -
940A LEU* 1.3 72.2 - - - +
942A GLY* 1.3 61.4 + - - +
944A CYS* 3.5 7.2 + - - +
945A ARG* 3.1 24.5 + - - +
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Residues in contact with GLY 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
938A PRO 3.1 7.5 + - - -
939A VAL 3.1 7.5 + - - -
941A SER* 1.3 73.7 - - - +
943A VAL* 1.3 64.2 + - - +
945A ARG* 3.3 14.4 + - - +
946A HIS* 3.1 20.1 + - - -
997A LEU* 3.7 25.8 - - - -
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Residues in contact with VAL 943 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A PHE* 4.0 31.9 - - + +
842A TYR* 5.7 0.2 - - + -
939A VAL* 3.0 19.3 + - + +
940A LEU* 3.5 12.1 - - + +
942A GLY* 1.3 74.1 - - - +
944A CYS* 1.3 69.0 + - - +
946A HIS* 2.9 23.7 + - - +
947A LEU* 3.2 30.0 + - + +
958A LEU* 5.7 0.7 - - + -
990A TRP* 4.4 15.7 - - + -
994A LEU* 4.0 26.7 - - + -
997A LEU* 4.0 5.1 - - + +
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Residues in contact with CYS 944 (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 TYR* 3.7 44.4 - - + -
845A LEU* 5.0 11.4 - - - -
846A LEU* 4.1 10.5 - - + -
887A LEU* 3.7 17.5 - - + -
890A ILE* 5.0 3.1 - - + -
940A LEU* 2.9 25.5 + - - +
941A SER* 3.6 6.7 - - - +
943A VAL* 1.3 79.6 - - - +
945A ARG* 1.3 62.7 + - - +
947A LEU* 3.2 3.0 + - - +
948A ALA* 2.9 27.4 + - - +
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Residues in contact with ARG 945 (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* 4.2 11.8 - - + -
884A GLU* 3.2 37.8 + - - +
887A LEU* 3.4 41.2 - - + +
888A GLN 5.3 1.2 - - - +
941A SER* 3.1 14.9 + - - +
942A GLY* 3.4 13.4 - - - +
943A VAL 3.1 0.4 + - - -
944A CYS* 1.3 74.9 - - - +
946A HIS* 1.3 66.9 + - + +
948A ALA* 4.1 1.7 - - - +
949A ALA* 3.0 35.5 + - + +
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Residues in contact with HIS 946 (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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942A GLY 3.1 27.8 + - - -
943A VAL* 2.9 7.8 + - - +
945A ARG* 1.3 80.6 - - + +
947A LEU* 1.3 61.2 + - - +
949A ALA* 3.8 4.2 - - - +
950A ASP* 2.9 32.3 + - - +
954A CYS* 3.8 19.6 - - - -
990A TRP* 4.0 23.3 - + + -
993A GLU* 3.5 38.8 + - + +
997A LEU* 5.3 1.9 - - + +
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Residues in contact with LEU 947 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A PHE* 4.1 15.0 - - + +
839A SER* 4.5 8.1 - - - -
842A TYR* 3.6 48.8 + - + -
870A LEU* 5.2 0.7 - - - +
943A VAL* 3.2 24.3 + - + +
944A CYS 3.8 6.3 - - - +
946A HIS* 1.3 78.4 - - - +
948A ALA* 1.3 58.1 + - - +
951A PHE* 3.2 49.4 + - + +
954A CYS* 4.2 22.7 - - + +
955A ARG* 4.5 2.0 - - - +
958A LEU* 5.3 6.3 - - + -
990A TRP* 4.3 13.0 - - + -
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Residues in contact with ALA 948 (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 TYR* 3.3 21.7 + - + +
846A LEU* 5.3 0.9 - - + -
870A LEU 5.1 1.4 - - - +
872A THR 5.3 1.6 - - - +
875A PHE* 3.6 29.4 - - + +
876A PHE* 3.8 28.0 + - + +
883A LEU* 4.5 9.6 - - + -
887A LEU* 5.6 2.0 - - + -
944A CYS 2.9 17.0 + - - +
945A ARG* 4.2 1.8 - - - +
947A LEU* 1.3 77.3 - - - +
949A ALA* 1.3 64.4 + - - +
950A ASP* 3.3 1.7 + - - -
951A PHE 4.5 1.0 + - - -
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Residues in contact with ALA 949 (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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872A THR 5.3 1.5 - - - +
873A ASP* 4.7 15.6 - - - +
876A PHE* 4.1 22.7 - - + +
945A ARG* 3.0 26.8 + - + +
946A HIS* 4.0 4.7 - - - +
948A ALA* 1.3 77.6 - - - +
950A ASP* 1.3 64.3 + - + +
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Residues in contact with ASP 950 (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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739A ARG* 3.2 33.1 + - - +
740A THR* 5.0 2.3 - - - +
872A THR 6.1 2.6 - - - -
873A ASP* 4.3 4.3 - - - +
946A HIS* 2.9 10.9 + - - +
948A ALA 3.3 0.6 - - - -
949A ALA* 1.3 84.5 - - + +
951A PHE* 1.3 67.3 + - - +
952A ARG* 2.9 9.0 - - - +
953A HIS* 2.8 46.0 + - - +
954A CYS* 3.1 22.8 + - - -
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Residues in contact with PHE 951 (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 SER* 4.2 14.6 - - - -
842A TYR* 4.7 1.1 - + - -
870A LEU* 3.9 26.0 + - + +
871A CYS* 3.8 22.3 - - - +
916A LEU* 3.8 32.1 - - + -
947A LEU* 3.2 49.2 + - + +
948A ALA 4.5 1.4 + - - -
950A ASP* 1.3 74.7 - - - +
952A ARG* 1.3 62.2 + - - +
954A CYS* 3.9 2.0 - - - -
955A ARG* 3.0 59.8 + - + +
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Residues in contact with ARG 952 (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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702A ASP* 3.1 46.5 + - + +
703A SER* 4.5 3.6 + - - -
871A CYS* 3.6 36.5 - - - +
872A THR* 5.6 0.7 - - - -
950A ASP* 2.8 9.3 + - - +
951A PHE* 1.3 81.6 - - - +
953A HIS* 1.3 79.9 + - + +
954A CYS 3.9 0.2 + - - -
955A ARG* 3.2 43.9 + - - +
986A LYS* 4.4 0.8 + - - +
0U T 3.6 27.1 + - - -
1U A 4.3 6.4 + - - -
2U G 3.7 20.5 + - - -
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Residues in contact with HIS 953 (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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702A ASP* 3.7 29.9 + - + +
737A GLU 4.4 5.6 + - - -
739A ARG* 3.4 38.5 + - + +
740A THR* 3.1 35.8 + - + +
742A HIS* 6.2 2.1 - + - -
950A ASP* 2.8 33.9 + - - +
952A ARG* 1.3 104.6 + - + +
954A CYS* 1.3 59.8 + - - +
955A ARG 3.9 0.4 - - - -
956A GLY 4.8 0.2 - - - +
986A LYS* 3.6 23.4 + - - +
0U T 4.9 5.2 + - - -
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Residues in contact with CYS 954 (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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740A THR* 4.3 13.5 - - - -
946A HIS* 3.8 33.4 - - - +
947A LEU* 4.2 14.7 - - + +
950A ASP* 3.1 28.2 + - - +
951A PHE 4.4 0.2 - - - +
953A HIS* 1.3 83.2 - - - +
955A ARG* 1.3 55.6 + - - +
956A GLY 2.6 20.5 + - - +
958A LEU* 4.9 1.0 - - - +
990A TRP* 3.1 36.4 + - + +
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Residues in contact with ARG 955 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A GLY* 4.6 8.3 - - - -
871A CYS* 3.9 24.5 - - - -
947A LEU* 4.5 4.5 - - - +
951A PHE* 3.0 53.2 + - + +
952A ARG* 3.2 45.2 + - - +
953A HIS 5.6 0.2 - - - -
954A CYS* 1.3 76.2 - - - +
956A GLY* 1.3 59.9 + - - +
957A GLY 4.2 0.5 + - - -
958A LEU* 4.4 12.2 - - - +
1U A 3.5 15.6 + - - -
2U G 2.6 28.5 + - - +
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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