Contacts of the helix formed by residues 957 - 975 (chain A) in PDB entry 6CNB
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 TYR 957 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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955A LEU* 6.0 0.2 - - - -
956A PRO* 1.3 77.7 - - + +
958A ALA* 1.3 77.5 + - + +
959A ILE 3.0 5.2 - - - -
960A MET* 2.7 35.6 + - + +
961A GLU* 3.3 15.5 + - + +
1031A LEU* 3.2 53.3 + - + +
1032A LEU 3.9 9.9 - - - +
1033A GLU 3.4 19.3 - - - +
1034A PRO* 3.9 6.3 - - + -
1035A PRO* 3.3 34.0 - - + +
1040A GLN* 2.5 34.8 + - - -
1044A PRO* 6.1 0.9 - - + -
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Residues in contact with ALA 958 (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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955A LEU* 3.1 29.1 + - + +
957A TYR* 1.3 88.7 - - + +
959A ILE* 1.3 64.7 + - - +
961A GLU* 3.0 20.8 + - + +
962A THR* 2.9 29.6 + - + +
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Residues in contact with ILE 959 (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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955A LEU* 2.7 41.4 + - + +
956A PRO* 3.4 20.9 - - + +
958A ALA* 1.3 72.3 - - - +
960A MET* 1.3 64.9 + - + +
962A THR* 2.9 7.0 + - - -
963A ALA* 2.9 29.3 + - - +
1012A ILE* 3.5 28.9 - - + +
1016A ALA* 3.7 20.6 - - + -
1019A LEU* 4.4 6.5 - - + -
1062A ILE* 4.3 30.7 - - + -
1067A VAL* 4.4 10.9 - - + +
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Residues in contact with MET 960 (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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956A PRO 5.0 2.0 - - - +
957A TYR* 2.7 22.1 + - + +
959A ILE* 1.3 90.4 - - + +
961A GLU* 1.3 65.9 + - - +
963A ALA* 4.1 6.7 - - + -
964A ASN* 2.9 41.0 + - - +
1009A ARG* 5.1 7.2 - - - +
1012A ILE* 3.7 7.9 - - + +
1013A ASN* 3.5 54.5 - - - +
1016A ALA* 4.1 6.7 - - + -
1032A LEU 5.1 7.9 - - - +
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Residues in contact with GLU 961 (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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957A TYR* 3.3 17.1 + - + +
958A ALA* 3.0 28.0 + - + +
960A MET* 1.3 79.0 - - - +
962A THR* 1.3 54.2 + - + +
964A ASN* 3.6 2.1 - - - +
965A GLU* 2.7 37.1 + - - +
1034A PRO* 5.0 9.2 - - - +
1035A PRO* 5.8 1.0 - - - +
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Residues in contact with THR 962 (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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955A LEU* 4.9 4.9 - - + +
958A ALA* 2.9 18.5 + - + +
959A ILE* 2.9 20.1 + - - -
961A GLU* 1.3 73.9 - - + +
963A ALA* 1.3 64.2 + - - +
965A GLU* 3.0 21.0 - - - +
966A ILE* 3.1 13.2 + - - +
1064A GLU* 3.8 31.0 - - - +
1067A VAL* 3.9 21.3 - - - +
1068A ARG* 5.0 14.1 - - + +
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Residues in contact with ALA 963 (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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959A ILE 2.9 19.6 + - - +
960A MET* 3.7 12.1 - - + +
961A GLU 3.2 0.2 - - - -
962A THR* 1.3 74.0 + - - +
964A ASN* 1.3 63.1 + - - +
966A ILE* 2.8 24.1 + - - +
967A LEU* 3.1 20.8 + - + +
1009A ARG* 5.2 4.7 - - + -
1012A ILE* 4.5 26.9 - - + -
1067A VAL* 4.7 2.2 - - + +
1071A LEU* 4.4 12.1 - - - -
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Residues in contact with ASN 964 (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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960A MET* 2.9 32.8 + - - +
961A GLU* 4.0 2.2 - - - +
963A ALA* 1.3 73.2 - - - +
965A GLU* 1.3 56.7 + - - +
966A ILE 3.2 0.2 - - - -
967A LEU* 3.9 6.2 - - - +
968A GLY* 2.9 29.7 + - - +
969A PRO* 4.4 0.5 - - - +
971A GLU* 5.3 0.7 - - - +
1009A ARG* 3.4 32.5 + - - +
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Residues in contact with GLU 965 (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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961A GLU 2.7 19.2 + - - +
962A THR* 3.0 20.0 - - - +
964A ASN* 1.3 72.8 - - - +
966A ILE* 1.3 60.9 + - + +
969A PRO* 3.1 24.5 - - - +
1068A ARG* 5.0 14.4 - - - +
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Residues in contact with ILE 966 (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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962A THR 3.1 11.8 + - - +
963A ALA 2.8 13.1 + - - +
965A GLU* 1.3 77.9 - - + +
967A LEU* 1.3 67.8 + - + +
968A GLY 3.2 1.3 + - - -
969A PRO* 3.4 13.0 - - - +
970A LEU* 3.6 26.5 - - + +
1067A VAL* 6.2 0.2 - - + -
1068A ARG* 4.4 24.5 - - + +
1071A LEU* 3.8 27.1 - - + -
1075A LEU* 4.4 14.4 - - + -
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Residues in contact with LEU 967 (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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963A ALA* 3.1 19.2 + - + +
964A ASN* 4.6 4.9 - - - +
966A ILE* 1.3 80.8 - - + +
968A GLY* 1.3 59.6 + - - +
970A LEU* 2.9 21.8 + - + -
971A GLU* 2.7 54.5 + - + +
1005A TYR* 4.1 25.4 - - + +
1008A LEU* 4.7 13.7 - - + -
1009A ARG* 3.5 45.8 - - + +
1012A ILE* 6.0 0.7 - - + -
1071A LEU* 5.4 6.7 - - + -
1075A LEU* 5.5 1.1 - - + -
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Residues in contact with GLY 968 (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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964A ASN* 2.9 18.3 + - - +
966A ILE 3.2 0.6 - - - -
967A LEU* 1.3 76.7 - - - +
969A PRO* 1.3 64.9 - - - +
970A LEU 2.9 6.2 + - - -
971A GLU* 4.6 6.7 + - - -
972A GLU* 3.1 32.9 + - - +
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Residues in contact with PRO 969 (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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964A ASN 4.4 0.2 - - - +
965A GLU* 3.1 26.0 - - - +
966A ILE 3.4 5.7 - - - +
968A GLY* 1.3 83.0 - - - +
970A LEU* 1.3 67.9 + - - +
972A GLU* 4.5 7.2 - - - +
973A ARG* 3.1 54.7 + - + +
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Residues in contact with LEU 970 (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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966A ILE* 3.6 16.6 - - + +
967A LEU* 2.9 23.4 + - + +
968A GLY 2.9 0.4 + - - -
969A PRO* 1.3 86.5 - - - +
971A GLU* 1.3 67.8 + - - +
972A GLU 3.4 0.9 - - - -
973A ARG* 2.9 23.7 + - - +
974A LEU* 3.1 10.6 + - - +
1005A TYR* 3.7 47.8 - - + +
1075A LEU* 4.1 20.0 - - + -
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Residues in contact with GLU 971 (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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964A ASN* 5.7 1.0 - - - +
967A LEU* 2.7 45.7 + - + +
968A GLY* 4.4 4.7 - - - +
970A LEU* 1.3 73.0 - - - +
972A GLU* 1.3 58.7 + - - +
974A LEU* 2.9 29.7 + - - +
975A VAL* 3.6 2.8 + - - +
1005A TYR* 4.7 22.7 - - + +
1006A HIS* 5.3 1.9 + - - -
1009A ARG* 2.8 33.1 + - - +
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Residues in contact with GLU 972 (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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968A GLY* 3.1 24.4 + - - +
969A PRO* 4.5 5.5 - - - +
971A GLU* 1.3 79.9 - - - +
973A ARG* 1.3 64.1 + - + +
974A LEU 3.0 0.2 - - - -
975A VAL* 3.0 32.9 + - - +
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Residues in contact with ARG 973 (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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969A PRO* 3.1 52.5 + - + +
970A LEU* 2.9 16.6 + - + +
972A GLU* 1.3 80.0 - - + +
974A LEU* 1.3 58.0 + - - +
975A VAL* 4.6 5.3 - - - +
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Residues in contact with LEU 974 (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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970A LEU 3.1 6.4 + - - +
971A GLU* 2.9 16.1 + - - +
973A ARG* 1.3 78.7 - - - +
975A VAL* 1.3 75.7 + - - +
976A ARG* 4.5 0.7 - - - -
998A TYR* 3.3 46.6 - - + +
1001A GLU* 4.6 14.8 - - + +
1002A ARG* 3.4 53.6 + - + +
1005A TYR* 5.8 5.6 - - + -
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Residues in contact with VAL 975 (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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971A GLU 3.6 1.8 + - - +
972A GLU* 3.0 25.7 + - - +
973A ARG* 4.6 5.2 - - - +
974A LEU* 1.3 95.3 - - - +
976A ARG* 1.3 84.1 + - - +
977A TYR* 4.1 27.8 - - + +
983A LEU* 5.6 9.0 - - + -
1002A ARG* 3.0 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
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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