Contacts of the helix formed by residues 934 - 947 (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 ASN 934 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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674A LYS* 6.2 1.2 - - - +
675A HIS* 6.1 1.2 - - - +
927A GLU* 4.7 4.4 - - + +
928A GLY* 4.6 27.2 + - - +
929A ASN* 5.7 5.2 - - - +
931A GLN 3.6 6.7 + - - -
933A VAL* 1.3 82.1 - - - +
935A PHE* 1.3 66.4 + - - +
936A ASN* 3.0 23.2 + - - +
937A ARG* 3.2 31.7 + - + +
938A SER* 3.5 7.6 + - - -
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Residues in contact with PHE 935 (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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931A GLN* 5.7 7.4 - - + -
933A VAL* 3.5 34.0 - - + +
934A ASN* 1.3 73.6 - - - +
936A ASN* 1.3 66.9 + - - +
938A SER* 3.9 3.4 - - - +
939A TRP* 3.0 24.8 + - - +
1004A PHE* 4.3 16.4 - + - -
1007A SER* 4.2 15.9 - - - -
1008A LEU* 3.4 48.5 - - + -
1011A TYR* 3.7 36.5 + + + -
1070A PHE* 4.1 8.6 - + + -
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Residues in contact with ASN 936 (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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627A ASP* 5.0 15.6 + - - +
934A ASN* 3.0 14.7 + - - +
935A PHE* 1.3 81.9 - - - +
937A ARG* 1.3 64.1 + - - +
939A TRP* 3.5 11.8 + - - +
940A ASP* 3.7 12.1 + - - +
1011A TYR* 4.3 9.5 + - - -
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Residues in contact with ARG 937 (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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625A ASN* 5.4 10.4 + - - +
626A LEU* 4.3 14.4 - - + +
627A ASP* 5.5 7.4 - - - +
674A LYS* 3.9 5.9 + - - +
675A HIS* 3.2 39.0 - - - +
676A SER 4.3 0.2 - - - +
679A TYR* 4.5 4.4 - - - -
680A THR* 2.5 43.3 + - - +
683A ARG* 5.6 1.2 - - - +
927A GLU* 3.4 27.6 + - - +
934A ASN* 3.2 28.6 + - + +
936A ASN* 1.3 80.5 - - - +
938A SER* 1.3 69.9 + - - +
940A ASP* 2.8 30.2 + - - +
941A HIS* 2.9 15.1 + - + +
1077A LYS* 4.7 6.1 - - - +
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Residues in contact with SER 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
933A VAL* 3.8 23.4 + - - +
934A ASN 3.5 6.0 + - - -
935A PHE 3.4 3.8 + - - -
937A ARG* 1.3 82.1 - - - +
939A TRP* 1.3 63.8 + - - +
941A HIS* 3.7 9.0 - - - +
942A ALA* 2.9 26.0 + - - +
1070A PHE* 3.8 12.6 - - - -
1073A ILE* 4.2 17.6 - - - +
1074A ALA 5.6 1.8 - - - -
1077A LYS* 3.4 25.3 + - - +
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Residues in contact with TRP 939 (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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935A PHE 3.0 18.1 + - - +
936A ASN 3.6 5.4 - - - +
938A SER* 1.3 77.0 - - - +
940A ASP* 1.3 73.7 + - - +
942A ALA* 3.6 2.8 + - + +
943A TYR* 3.1 34.3 + + + +
959A ILE* 6.6 0.2 - - + -
1011A TYR* 3.7 11.0 - + - +
1012A ILE* 5.5 9.0 - - + -
1015A LYS* 3.4 47.7 - - + +
1062A ILE* 3.9 38.6 - - + -
1066A SER* 4.7 10.3 - - - -
1067A VAL* 4.7 11.9 - - + -
1070A PHE* 3.4 50.8 - + + -
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Residues in contact with ASP 940 (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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625A ASN* 3.0 23.7 + - + +
626A LEU* 5.4 10.2 - - - +
627A ASP* 5.5 5.9 - - - +
655A ARG* 4.1 24.5 + - - +
936A ASN* 4.2 12.5 - - - +
937A ARG* 2.8 17.7 + - - +
939A TRP* 1.3 83.3 - - - +
941A HIS* 1.3 58.1 + - - +
943A TYR* 2.5 38.4 + - - +
944A ASN 3.2 1.4 + - - -
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Residues in contact with HIS 941 (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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623A VAL 3.7 11.0 + - - -
624A ILE* 4.8 1.6 - - - -
625A ASN* 3.1 33.6 + - - +
680A THR* 5.4 7.9 - - + -
684A ASP* 2.9 36.9 + - + -
685A TYR* 4.8 1.3 - + - -
937A ARG* 2.9 19.0 + - + +
938A SER* 3.1 13.4 + - - +
940A ASP* 1.3 72.0 - - - +
942A ALA* 1.3 59.7 + - - +
944A ASN* 3.7 0.5 - - - +
945A ILE* 3.1 46.2 - - + +
1073A ILE* 4.8 25.1 - - + +
1077A LYS* 6.0 4.5 - - - +
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Residues in contact with ALA 942 (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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938A SER 2.9 15.6 + - - +
939A TRP* 3.6 6.1 - - + +
940A ASP 2.8 0.2 + - - -
941A HIS* 1.3 76.8 + - - +
943A TYR* 1.3 66.3 + - - +
945A ILE* 3.2 5.9 + - - +
946A THR* 2.9 26.5 + - - +
1066A SER 3.9 10.3 - - - +
1069A LYS* 4.3 9.2 - - + +
1070A PHE* 3.8 34.8 - - + +
1073A ILE* 5.4 5.1 - - + +
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Residues in contact with TYR 943 (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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655A ARG* 5.4 10.1 - - - -
939A TRP* 3.1 28.1 + + + +
940A ASP* 2.5 22.0 + - + +
942A ALA* 1.3 74.4 - - - +
944A ASN* 1.3 68.4 + - + +
945A ILE 2.9 2.1 + - - -
946A THR* 3.2 6.8 - - + +
947A PHE* 2.5 62.1 + + + -
1061A ARG* 3.5 34.9 + - + +
1062A ILE* 5.8 0.4 - - + -
1066A SER* 4.9 11.9 - - - +
136H LYS* 2.9 33.1 + - - -
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Residues in contact with ASN 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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623A VAL* 5.0 3.2 - - - +
624A ILE 3.5 3.8 + - - -
625A ASN* 2.7 41.9 + - - +
655A ARG* 4.0 11.0 - - + +
656A GLY* 3.0 34.0 - - - +
940A ASP 3.2 2.5 + - - +
941A HIS 3.7 4.5 - - - +
943A TYR* 1.3 86.8 - - + +
945A ILE* 1.3 70.5 + - - +
947A PHE* 3.6 18.7 - - + +
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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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623A VAL* 4.2 24.7 - - + -
625A ASN* 5.9 0.2 - - - +
685A TYR* 5.1 2.7 - - - +
941A HIS* 3.1 46.9 - - + +
942A ALA* 3.2 7.4 + - - +
943A TYR 2.9 1.8 + - - -
944A ASN* 1.3 87.8 + - - +
946A THR* 1.3 61.3 + - - +
947A PHE 3.0 13.8 + - - +
1069A LYS* 5.7 10.3 - - + -
1073A ILE* 6.4 0.2 - - + -
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Residues in contact with THR 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 ALA 2.9 23.7 + - - +
943A TYR* 3.2 13.0 - - + +
945A ILE* 1.3 73.1 - - - +
947A PHE* 1.3 66.2 + - - +
948A ASN* 3.3 7.6 + - - +
1063A SER* 4.4 4.5 + - - +
1065A LYS* 3.1 44.5 - - - +
1066A SER* 3.4 31.7 + - - +
1069A LYS* 4.3 11.2 - - - +
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Residues in contact with PHE 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 TYR* 2.5 46.6 + + + +
944A ASN* 3.6 21.7 - - + +
945A ILE 3.0 6.7 - - - +
946A THR* 1.3 76.1 - - - +
948A ASN* 1.3 60.8 + - - +
949A ASN* 3.9 18.4 - - + -
1061A ARG* 3.0 29.4 - - - -
136H LYS* 3.4 47.1 - - + -
137H GLN* 6.3 0.2 - - - -
138H GLU* 5.5 7.0 - - - -
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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