Contacts of the helix formed by residues 980 - 997 (chain A) in PDB entry 6DBT
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 980 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616A LYS* 6.3 0.2 - - - -
618A SER* 4.5 5.9 + - - -
620A ASP* 4.7 14.9 + - - +
727A THR 4.9 0.7 - - - -
728A GLY* 3.7 37.1 + - - -
729A TYR* 4.0 9.7 + - - -
730A ASP 5.0 1.1 + - - -
814A ASP* 3.8 17.8 + - - -
978A TRP 3.2 4.4 + - - -
979A ALA* 1.3 71.0 - - - +
981A GLU* 1.3 65.5 + - - +
983A ASN* 2.9 18.5 + - - +
984A GLU* 3.4 8.3 + - - +
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Residues in contact with GLU 981 (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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669A ASN* 3.4 26.4 + - - +
816A LEU* 3.6 50.2 - - + +
979A ALA* 3.1 6.8 - - + +
980A SER* 1.3 75.7 - - - +
982A GLY* 1.3 83.3 + - - +
984A GLU* 2.9 9.9 + - + +
985A SER* 2.8 28.8 + - - +
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Residues in contact with GLY 982 (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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616A LYS* 5.8 1.8 - - - -
668A PRO 5.3 0.9 - - - -
669A ASN* 3.0 33.2 - - - +
671A GLU* 3.9 8.9 - - - +
674A CYS* 4.9 3.6 - - - -
979A ALA 3.8 5.8 + - - -
980A SER 3.0 2.6 + - - -
981A GLU* 1.3 83.5 + - - +
983A ASN* 1.3 60.8 + - - -
985A SER* 3.0 21.6 + - - -
986A GLY 3.2 4.0 + - - -
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Residues in contact with ASN 983 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LYS* 5.7 3.4 - - - +
618A SER* 2.5 35.1 + - - +
620A ASP* 3.9 17.1 - - + +
622A MET* 6.2 0.2 - - - +
641A ARG* 2.6 86.4 + - - +
643A SER* 3.1 14.5 + - - -
674A CYS* 3.9 18.3 - - - -
979A ALA 5.1 0.4 + - - -
980A SER* 2.9 11.8 + - - +
982A GLY* 1.3 71.3 - - - -
984A GLU* 1.3 55.3 + - - +
986A GLY* 2.9 7.3 + - - +
987A ASN* 2.9 0.6 - - - +
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Residues in contact with GLU 984 (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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620A ASP* 2.6 27.9 + - - +
621A GLY 4.0 2.6 - - - +
816A LEU* 6.1 4.0 - - + +
980A SER* 3.4 6.7 + - - +
981A GLU* 2.9 16.4 + - + +
983A ASN* 1.3 75.1 - - - +
985A SER* 1.3 68.1 + - - +
987A ASN* 2.8 45.3 + - - +
988A LYS 4.4 0.2 + - - -
1102A CA 2.8 24.5 - - - -
35F T 4.6 8.5 + - - +
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Residues in contact with SER 985 (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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669A ASN 5.2 0.4 - - - -
671A GLU* 3.2 23.5 + - - +
981A GLU* 2.8 22.6 + - - -
982A GLY* 3.0 16.4 - - - -
984A GLU* 1.3 73.0 - - - +
986A GLY* 1.3 50.9 + - - -
987A ASN 2.8 11.8 + - - -
988A LYS* 3.0 45.0 + - - +
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Residues in contact with GLY 986 (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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641A ARG* 2.9 24.2 + - - -
671A GLU* 4.0 13.6 - - - +
674A CYS* 6.4 0.9 - - - -
982A GLY 3.2 3.8 + - - -
983A ASN* 2.9 7.1 + - - -
985A SER* 1.3 78.2 + - - +
987A ASN* 1.3 63.4 + - - +
988A LYS 3.3 0.2 - - - -
989A LEU* 3.0 31.5 + - - +
990A PHE 3.2 3.6 + - - -
1013A HIS* 4.6 2.8 + - - -
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Residues in contact with ASN 987 (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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620A ASP* 4.7 2.2 + - - +
621A GLY 4.0 7.5 + - - -
622A MET* 3.2 34.2 - - - +
641A ARG* 2.6 30.3 + - - +
983A ASN* 2.9 5.2 - - - +
984A GLU* 2.8 48.7 + - - +
985A SER 2.8 5.1 + - - -
986A GLY* 1.3 71.6 - - - +
988A LYS* 1.3 63.2 + - - +
989A LEU 2.9 1.6 + - - -
990A PHE* 2.9 12.3 + - - +
991A ARG* 3.2 34.3 + - - +
35F T 5.0 2.0 + - - -
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Residues in contact with LYS 988 (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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671A GLU* 3.0 30.7 + - - +
985A SER* 3.0 31.2 + - - +
987A ASN* 1.3 78.2 - - - +
989A LEU* 1.3 73.1 + - + +
991A ARG* 3.2 18.9 - - - +
992A ARG* 3.4 22.9 + - - +
20E A 3.6 42.2 - - - +
21E G 4.4 17.4 + - - +
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Residues in contact with LEU 989 (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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494A PHE* 4.6 15.7 - - + -
671A GLU* 4.5 21.3 - - + +
986A GLY* 3.0 18.7 + - - +
987A ASN 2.9 0.6 + - - -
988A LYS* 1.3 89.3 - - + +
990A PHE* 1.3 55.5 + - - +
992A ARG* 2.9 8.8 + - - +
993A PHE* 2.6 49.5 + - + +
1013A HIS* 4.2 23.3 - - + +
1016A TYR* 3.4 44.2 - - + +
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Residues in contact with PHE 990 (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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622A MET* 3.7 25.4 - - + -
625A VAL* 3.8 23.6 - - + -
639A ALA* 4.3 18.4 - - + -
641A ARG* 4.1 15.9 - - - +
679A LEU* 3.4 30.1 - - + -
681A PHE* 4.4 22.4 - + - -
986A GLY 3.2 2.0 + - - +
987A ASN 2.9 7.2 + - - +
989A LEU* 1.3 77.1 - - - +
991A ARG* 1.3 69.2 + - - +
993A PHE* 2.9 10.4 + - - +
994A ARG* 2.9 23.3 + - + +
1006A LEU* 4.5 3.4 - - + -
1009A ILE* 3.5 40.4 - - + -
1013A HIS* 5.0 8.0 - + + -
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Residues in contact with ARG 991 (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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622A MET* 4.0 21.4 - - + +
623A GLY 4.1 9.7 + - - -
624A ASP 5.4 1.6 + - - -
625A VAL* 4.2 23.1 - - + +
626A SER* 5.9 1.1 - - - +
987A ASN* 3.2 48.4 + - - +
988A LYS* 3.2 18.9 - - - +
990A PHE* 1.3 83.3 - - + +
992A ARG* 1.3 65.9 + - + +
994A ARG* 3.0 25.3 + - - +
995A LYS* 3.5 5.4 + - - +
21E G 6.0 2.0 - - - -
34F G 3.8 42.5 + - - -
35F T 4.3 3.2 + - - -
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Residues in contact with ARG 992 (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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494A PHE* 3.1 43.9 - - - -
988A LYS 3.4 16.7 + - - +
989A LEU* 2.9 7.3 + - - +
991A ARG* 1.3 82.1 - - + +
993A PHE* 1.3 66.1 + - - +
995A LYS* 3.0 25.9 + - - +
996A MET* 3.5 42.3 + - + +
21E G 3.0 60.1 + - - +
22E T 5.3 2.0 + - - -
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Residues in contact with PHE 993 (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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491A VAL* 5.0 8.3 - - + -
494A PHE* 4.4 31.9 - + - -
989A LEU* 2.6 34.1 + - + +
990A PHE* 2.9 12.8 + - - +
992A ARG* 1.3 75.3 - - - +
994A ARG* 1.3 60.7 + - - +
995A LYS 3.5 0.2 + - - -
996A MET* 5.1 0.7 - - - +
997A ASN* 3.6 32.3 + - + +
1009A ILE* 4.3 21.6 - - + +
1012A HIS* 3.5 46.4 - - + -
1013A HIS* 4.2 22.2 - - + -
1016A TYR* 4.3 22.2 - + + -
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Residues in contact with ARG 994 (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 VAL* 2.9 48.4 + - + +
627A GLU* 5.3 21.8 - - + +
636A PRO* 4.0 25.0 + - - +
681A PHE* 5.1 6.6 - - - -
990A PHE* 2.9 13.9 + - + +
991A ARG* 3.0 17.2 + - - +
993A PHE* 1.3 78.5 - - - +
995A LYS* 1.3 62.7 + - - +
998A ALA* 3.5 21.9 + - - +
1002A LYS* 5.8 2.4 - - - +
1005A GLU* 2.6 42.4 + - - +
1009A ILE* 3.8 19.0 - - + +
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Residues in contact with LYS 995 (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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626A SER 5.8 3.4 - - - -
627A GLU* 6.2 4.3 - - + +
991A ARG 3.5 5.6 + - - +
992A ARG* 3.0 17.9 + - - +
994A ARG* 1.3 84.4 - - - +
996A MET* 1.3 87.9 + - + +
997A ASN 3.9 0.2 + - - -
998A ALA* 4.4 6.6 + - - +
628C LYS* 6.3 2.5 - - - +
995C LYS* 4.8 19.4 - - + +
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Residues in contact with MET 996 (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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494A PHE* 4.6 23.3 - - + +
496A SER* 4.6 5.8 - - - -
992A ARG* 3.5 48.8 + - + +
993A PHE* 5.5 0.4 - - - +
995A LYS* 1.3 99.7 - - + +
997A ASN* 1.3 71.4 + - - +
998A ALA 3.5 2.0 + - - -
499C GLN* 5.7 2.9 - - - -
996C MET* 6.6 0.7 - - + -
21E G 5.9 0.2 - - - +
22E T 5.2 8.1 - - - +
22G T 4.1 20.1 + - - +
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Residues in contact with ASN 997 (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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491A VAL* 6.0 0.8 - - - +
494A PHE* 4.1 16.2 + - - +
495A LEU 4.3 13.5 + - - -
496A SER* 4.8 4.5 - - - +
497A CYS* 5.9 0.2 - - - -
993A PHE* 3.6 30.6 + - + +
995A LYS 3.6 0.2 - - - -
996A MET* 1.3 95.3 - - - +
998A ALA* 1.3 65.4 + - - +
1005A GLU 5.7 0.2 - - - +
1008A ASP* 4.4 15.5 - - - +
1009A ILE* 5.2 5.2 + - - +
1012A HIS* 2.9 38.4 + - + +
22G T 4.4 0.4 - - - -
23G G 3.5 19.8 + - - +
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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