Contacts of the helix formed by residues 943 - 956 (chain A) in PDB entry 4N78
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 943 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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939A SER 3.1 17.0 + - - -
940A LEU 3.2 2.2 + - - -
941A LEU 3.2 0.4 - - - -
942A GLN* 1.3 79.4 - - - +
944A THR* 1.3 65.0 + - - -
945A ILE 3.4 0.7 - - - -
946A LEU* 3.4 3.3 + - - +
947A GLN* 3.0 24.4 + - - +
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Residues in contact with THR 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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939A SER 4.2 2.0 + - - -
940A LEU* 3.5 18.1 + - + +
943A GLY* 1.3 71.0 - - - -
945A ILE* 1.3 64.0 + - - +
947A GLN* 3.2 15.1 + - - +
948A TYR* 3.0 37.7 + - + -
992A VAL* 5.4 0.9 - - + -
996A ASN* 3.2 28.6 + - - +
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Residues in contact with ILE 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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940A LEU* 3.0 22.3 + - + +
941A LEU* 4.1 9.6 - - + -
944A THR* 1.3 75.8 + - - +
946A LEU* 1.3 58.9 + - - +
948A TYR* 3.2 5.8 + - - +
949A VAL* 2.8 47.7 + - + +
993A CYS* 5.4 2.2 - - - +
996A ASN* 3.6 33.2 - - + +
997A LEU* 4.0 27.8 - - + +
1000A VAL* 3.9 28.5 - - + -
1109A TRP* 4.2 13.2 - - + -
1127A PHE* 6.0 0.4 - - + -
1164A ILE* 5.2 1.1 - - + -
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Residues in contact with LEU 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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941A LEU 3.0 19.7 + - - +
942A GLN* 3.8 24.0 - - + +
943A GLY 3.4 7.4 + - - +
945A ILE* 1.3 77.0 - - - +
947A GLN* 1.3 64.1 + - - +
949A VAL* 3.2 4.1 + - + +
950A LYS* 3.0 43.9 + - + +
1106A ASP* 4.0 23.8 - - + +
1108A ILE* 3.5 31.6 - - + -
1109A TRP* 4.0 18.4 - - + +
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Residues in contact with GLN 947 (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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943A GLY 3.0 13.2 + - - +
944A THR* 3.2 20.9 + - - +
946A LEU* 1.3 78.5 - - - +
948A TYR* 1.3 72.8 + - + +
950A LYS* 3.4 8.9 + - - +
951A THR* 3.0 34.5 + - - +
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Residues in contact with TYR 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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944A THR* 3.0 33.0 + - + +
945A ILE* 3.9 4.7 - - - +
947A GLN* 1.3 94.0 - - + +
949A VAL* 1.3 61.2 + - + +
951A THR* 3.7 5.7 - - - -
952A LEU* 2.9 36.2 + - - +
986A TYR* 3.2 34.1 - + - -
988A GLU* 2.2 34.1 + - + -
992A VAL* 3.6 30.2 - - + +
993A CYS* 3.5 31.2 - - - -
996A ASN* 5.4 0.2 - - - -
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Residues in contact with VAL 949 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945A ILE* 2.8 39.0 + - + +
946A LEU* 3.2 6.9 + - - +
948A TYR* 1.3 78.1 - - + +
950A LYS* 1.3 57.1 + - - +
952A LEU* 3.9 1.0 - - + -
953A MET* 2.9 42.1 + - + +
1108A ILE* 4.3 21.3 - - + +
1109A TRP* 4.0 23.8 - - + -
1127A PHE* 4.3 11.4 - - + -
1130A LEU* 4.1 26.6 - - + +
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Residues in contact with LYS 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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946A LEU* 3.0 46.1 + - + +
947A GLN* 3.8 7.2 - - - +
949A VAL* 1.3 75.2 - - - +
951A THR* 1.3 62.2 - - - +
953A MET* 3.7 7.6 + - - +
954A GLU* 3.8 17.0 + - - +
1106A ASP* 4.4 16.3 + - - +
1108A ILE* 3.7 31.5 - - + +
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Residues in contact with THR 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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947A GLN* 3.0 24.5 + - - +
948A TYR* 3.7 8.7 - - - -
949A VAL 3.2 0.2 - - - -
950A LYS* 1.3 74.9 - - - +
952A LEU* 1.3 65.6 + - - +
954A GLU* 3.2 15.5 + - - +
955A VAL* 3.4 17.2 + - + +
986A TYR* 4.0 26.9 - - + +
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Residues in contact with LEU 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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948A TYR* 2.9 21.5 + - - +
949A VAL 4.2 1.3 - - - +
951A THR* 1.3 74.2 - - - +
953A MET* 1.3 59.7 + - - +
954A GLU 3.1 0.2 - - - -
955A VAL* 3.1 9.2 + - + +
956A MET* 2.8 29.3 + - - +
983A ILE* 4.0 21.6 - - + +
986A TYR* 3.6 46.7 - - + -
989A LEU* 4.2 7.6 - - + -
993A CYS* 3.8 20.0 - - - -
1130A LEU* 3.9 17.6 - - + +
1134A MET* 3.6 30.1 - - + -
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Residues in contact with MET 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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949A VAL* 2.9 25.4 + - + +
950A LYS* 3.8 9.2 - - - +
951A THR 3.2 0.2 - - - -
952A LEU* 1.3 77.3 - - - +
954A GLU* 1.3 62.2 + - + +
956A MET* 3.2 25.7 - - - +
958A LYS* 4.8 3.8 + - - +
1108A ILE* 4.2 23.8 - - + +
1124A CYS 3.5 26.5 - - - +
1125A VAL* 4.2 16.2 - - + +
1126A GLU 4.1 15.9 - - - +
1127A PHE* 4.5 2.2 - - - -
1130A LEU* 3.6 38.8 - - + -
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Residues in contact with GLU 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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950A LYS 3.9 11.9 - - - +
951A THR* 3.2 9.0 + - - +
952A LEU 3.1 0.2 - - - -
953A MET* 1.3 77.9 - - + +
955A VAL* 1.3 65.7 + - + +
956A MET 3.1 8.8 + - - +
958A LYS* 2.7 37.2 + - - +
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Residues in contact with VAL 955 (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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951A THR* 3.4 22.7 - - + +
952A LEU* 3.1 19.4 + - + +
954A GLU* 1.3 76.4 - - + +
956A MET* 1.3 64.3 + - - +
957A PRO* 3.7 2.8 - - - +
982A ASP* 3.3 52.1 - - + +
983A ILE* 4.1 8.7 - - + +
986A TYR* 5.2 7.6 - - + -
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Residues in contact with MET 956 (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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952A LEU 2.8 8.7 + - - +
953A MET* 3.2 24.8 - - - +
954A GLU 3.1 9.4 - - - +
955A VAL* 1.3 81.1 - - - +
957A PRO* 1.3 75.4 - - + +
958A LYS* 3.3 9.2 + - - +
980A LEU* 4.3 6.3 - - + -
983A ILE* 4.2 11.0 - - - -
1124A CYS* 3.6 31.6 - - + +
1129A ARG 3.2 34.3 - - - +
1130A LEU* 4.2 13.9 - - - -
1133A ALA* 3.4 26.2 - - + -
1179A PHE* 4.1 11.9 - - + -
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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