Contacts of the helix formed by residues 980 - 998 (chain C) in PDB entry 6DBV
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618C SER* 4.4 8.3 - - - -
620C ASP* 5.8 4.3 - - - +
728C GLY* 3.3 39.5 - - - -
729C TYR* 4.1 6.5 - - - -
730C ASP* 5.1 4.3 + - - +
814C ASP* 5.6 1.7 + - - -
978C TRP 3.8 0.2 + - - -
979C ALA* 1.3 72.1 - - - +
981C GLU* 1.3 66.5 + - - +
982C GLY 3.0 4.6 + - - -
983C ASN* 3.0 16.0 + - - +
984C GLU* 3.5 8.7 + - - +
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Residues in contact with GLU 981 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C ASN* 4.1 22.9 - - + +
816C LEU* 4.2 38.2 - - + +
979C ALA* 3.4 13.6 - - + +
980C SER* 1.3 75.9 + - - +
982C GLY* 1.3 70.5 + - - +
984C GLU* 3.0 21.9 + - + +
985C SER* 3.2 15.7 + - - -
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Residues in contact with GLY 982 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616C LYS* 6.0 2.4 - - - +
668C PRO 5.2 2.0 - - - -
669C ASN* 3.1 31.4 + - - +
671C GLU* 4.1 8.1 - - - +
674C CYS* 5.1 7.4 - - - -
979C ALA 4.6 3.4 + - - -
980C SER* 3.0 2.4 + - - +
981C GLU* 1.3 79.1 + - - +
983C ASN* 1.3 64.1 + - - +
985C SER* 2.9 16.6 + - - -
986C GLY* 3.0 9.7 + - - -
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Residues in contact with ASN 983 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618C SER* 2.3 43.0 + - - +
619C CYS* 3.8 4.4 - - - +
620C ASP* 4.4 13.0 - - + +
641C ARG* 3.3 34.0 + - - +
643C SER* 3.0 22.1 + - - -
674C CYS* 3.1 18.6 - - - -
980C SER* 3.0 12.7 + - - +
982C GLY* 1.3 73.9 - - - +
984C GLU* 1.3 64.4 + - - +
986C GLY* 2.9 12.1 + - - +
987C ASN* 3.0 11.7 + - - +
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Residues in contact with GLU 984 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C ASP* 3.1 25.3 - - - +
816C LEU* 5.4 12.3 - - + -
980C SER* 3.5 6.9 + - - +
981C GLU* 3.0 18.2 + - + +
983C ASN* 1.3 77.7 - - - +
985C SER* 1.3 61.2 + - - +
987C ASN* 3.8 20.6 + - - +
988C LYS* 4.5 1.2 + - - +
1102C CA 3.1 16.2 - - - -
46H T 4.3 18.5 - - - +
47H A 5.4 0.2 + - - -
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Residues in contact with SER 985 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669C ASN 5.3 0.7 - - - -
671C GLU* 2.8 34.4 + - - +
981C GLU* 3.2 16.7 + - - -
982C GLY* 2.9 12.5 + - - -
984C GLU* 1.3 74.5 - - - +
986C GLY* 1.3 66.2 + - - +
987C ASN 2.9 4.2 + - - -
988C LYS* 3.0 28.3 + - - +
989C LEU 4.0 0.3 + - - -
20G A 5.6 4.4 + - - -
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Residues in contact with GLY 986 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641C ARG* 3.5 15.3 + - - -
671C GLU* 3.8 21.5 - - - +
674C CYS* 6.6 0.4 - - - -
982C GLY 3.0 8.4 + - - -
983C ASN* 2.9 7.9 + - - -
985C SER* 1.3 75.7 - - - +
987C ASN* 1.3 62.6 + - - +
989C LEU* 2.9 28.0 + - - +
990C PHE 3.2 3.5 + - - -
1013C HIS* 4.3 5.1 + - - -
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Residues in contact with ASN 987 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620C ASP* 5.5 4.7 - - - +
621C GLY* 4.2 5.7 + - - +
622C MET* 3.1 56.7 + - + +
641C ARG* 2.0 40.8 + - - +
983C ASN 3.0 4.1 + - - +
984C GLU* 3.8 25.0 + - - +
985C SER 2.9 0.2 + - - -
986C GLY* 1.3 73.1 - - - +
988C LYS* 1.3 67.0 + - - +
990C PHE* 2.9 16.9 + - - +
991C ARG* 3.0 17.3 + - - +
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Residues in contact with LYS 988 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C PHE* 5.6 5.6 - - - -
671C GLU* 4.4 15.3 + - - +
984C GLU 4.5 1.6 + - - +
985C SER* 3.0 16.3 + - - +
987C ASN* 1.3 79.1 - - - +
989C LEU* 1.3 78.4 + - + +
991C ARG* 3.0 24.2 + - - +
992C ARG* 3.1 17.3 + - + +
20G A 3.8 30.0 + - - +
21G G 3.1 32.1 - - - +
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Residues in contact with LEU 989 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494C PHE* 4.5 20.6 - - + -
671C GLU* 3.9 29.2 - - + +
985C SER 5.4 0.2 - - - +
986C GLY* 2.9 13.6 + - - +
988C LYS* 1.3 90.5 - - + +
990C PHE* 1.3 65.2 + - - +
992C ARG* 3.0 8.1 + - - +
993C PHE* 2.9 33.3 + - + +
1013C HIS* 3.4 28.9 - - + +
1016C TYR* 3.4 47.1 - - + +
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Residues in contact with PHE 990 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
622C MET* 3.9 14.4 - - + -
625C VAL* 4.6 13.5 - - + -
639C ALA* 3.8 30.1 - - + -
641C ARG* 4.4 19.3 - - + +
679C LEU* 3.4 35.9 - - + -
681C PHE* 4.3 13.9 - + - -
986C GLY 3.2 3.1 + - - +
987C ASN* 2.9 21.1 + - - +
989C LEU* 1.3 75.6 - - - +
991C ARG* 1.3 74.5 + - - +
993C PHE* 3.0 6.4 + - - +
994C ARG* 3.0 37.5 + - - +
1006C LEU* 4.6 2.7 - - + -
1009C ILE* 4.4 17.2 - - + +
1013C HIS* 4.6 8.3 - + + -
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Residues in contact with ARG 991 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622C MET* 2.6 54.3 - - + +
623C GLY 4.9 0.2 + - - -
625C VAL* 4.0 8.1 - - + +
626C SER* 3.6 14.5 + - - +
987C ASN 3.0 15.9 - - - +
988C LYS* 3.0 17.9 + - - +
990C PHE* 1.3 82.7 - - - +
992C ARG* 1.3 66.5 + - + +
994C ARG* 3.0 6.5 + - - +
995C LYS* 2.9 21.5 + - - +
21G G 6.0 2.0 - - - -
44H T 3.6 3.2 + - - -
45H G 2.3 57.5 + - - -
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Residues in contact with ARG 992 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A GLN* 4.5 11.1 - - - +
494C PHE* 3.2 59.2 - - + +
988C LYS* 3.1 13.9 + - + +
989C LEU 3.0 5.6 + - - +
991C ARG* 1.3 80.9 - - + +
993C PHE* 1.3 64.7 + - - +
995C LYS* 3.0 23.0 + - - +
996C MET* 2.9 45.7 + - - +
21G G 3.1 48.1 + - - +
22G T 3.6 25.1 + - - -
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Residues in contact with PHE 993 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491C VAL* 4.5 11.7 - - + -
494C PHE* 3.5 43.1 - + - -
989C LEU* 2.9 15.7 + - + +
990C PHE* 3.5 8.7 - - - +
992C ARG* 1.3 76.5 - - - +
994C ARG* 1.3 55.4 + - - +
996C MET 3.0 0.7 + - - -
997C ASN* 2.6 47.8 + - + +
998C ALA 3.7 0.7 + - - -
1009C ILE* 4.1 21.1 - - + -
1012C HIS* 3.4 24.2 - + + -
1013C HIS* 3.3 49.1 - + + -
1016C TYR* 4.3 16.6 - + + -
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Residues in contact with ARG 994 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625C VAL* 4.1 13.4 - - - +
626C SER 4.5 0.8 + - - -
627C GLU* 3.0 40.3 + - + +
636C PRO* 3.3 26.2 - - - +
681C PHE* 3.5 23.1 - - - -
990C PHE* 3.0 28.6 + - - +
991C ARG* 3.0 11.3 + - - +
993C PHE* 1.3 75.0 - - - +
995C LYS* 1.3 62.9 + - - +
996C MET 3.4 0.3 + - - -
998C ALA* 3.6 19.7 + - + +
1002C LYS* 5.3 2.8 - - - +
1005C GLU* 2.2 48.2 + - + +
1009C ILE* 3.6 21.6 - - + +
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Residues in contact with LYS 995 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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995A LYS* 5.5 11.2 - - + +
996A MET* 5.7 4.7 - - + +
628C LYS* 4.3 34.4 - - + +
991C ARG 2.9 12.7 + - - +
992C ARG* 3.0 24.6 + - - +
994C ARG* 1.3 78.6 - - - +
996C MET* 1.3 80.8 + - + +
22E T 5.7 0.3 + - - -
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Residues in contact with MET 996 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A GLN* 5.1 7.0 - - - +
996A MET* 3.7 42.6 - - + -
494C PHE* 4.3 28.0 - - + +
496C SER* 4.3 12.1 - - - -
499C GLN* 6.0 4.9 - - - +
992C ARG* 2.9 36.6 + - - +
995C LYS* 1.3 103.6 - - + +
997C ASN* 1.3 78.7 + - - +
22E T 4.9 14.1 + - - +
23E G 4.5 0.3 + - - -
22G T 6.0 0.2 - - - +
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Residues in contact with ASN 997 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494C PHE* 3.7 19.2 + - - +
495C LEU 4.8 0.6 + - - -
496C SER* 4.3 12.9 - - - +
497C CYS 5.2 0.2 - - - +
993C PHE* 2.6 33.0 + - + +
995C LYS 3.8 0.2 - - - -
996C MET* 1.3 89.7 + - - +
998C ALA* 1.3 68.0 + - - +
999C ARG 3.6 0.9 + - - -
1008C ASP* 4.0 19.1 - - + +
1009C ILE* 5.5 4.7 - - + -
1012C HIS* 3.0 36.0 - - + +
22E T 3.9 2.7 - - - +
23E G 2.5 36.1 + - - +
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Residues in contact with ALA 998 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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993C PHE 3.7 4.2 + - - -
994C ARG* 3.6 20.3 + - - +
995C LYS 5.2 0.2 - - - -
996C MET 4.0 0.2 - - - -
997C ASN* 1.3 80.2 - - - +
999C ARG* 1.3 58.6 + - - +
1000C GLN* 3.2 11.0 + - - +
1005C GLU* 3.9 36.6 - - + +
1008C ASP* 5.2 0.2 - - - -
1009C ILE* 5.3 2.0 - - - +
22E T 3.3 22.7 - - - +
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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