Contacts of the helix formed by residues 1001 - 1017 (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 SER1001 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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999C ARG 3.3 5.3 - - - +
1000C GLN* 1.3 81.7 - - - +
1002C LYS* 1.3 52.5 + - - +
1003C THR* 2.3 32.4 + - - -
1004C PHE* 2.6 21.4 + - - +
1005C GLU* 2.5 36.7 + - - +
30F C 3.8 31.9 - - - -
31F T 4.4 7.2 + - - -
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Residues in contact with LYS1002 (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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572C ILE* 3.5 39.4 - - + +
574C ARG* 5.2 0.2 - - - -
634C ALA* 3.1 41.8 + - + +
635C VAL* 4.5 12.0 - - + +
681C PHE* 4.7 14.4 - - + -
994C ARG* 5.3 1.8 - - - +
1000C GLN 4.3 0.2 - - - -
1001C SER* 1.3 71.0 + - - +
1003C THR* 1.3 62.7 - - - +
1005C GLU* 3.5 31.1 + - - +
1006C LEU* 4.2 6.1 + - - +
31F T 5.6 7.8 + - - -
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Residues in contact with THR1003 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572C ILE* 4.6 14.8 - - + -
574C ARG* 2.3 40.4 + - - +
1001C SER* 2.3 29.5 + - - +
1002C LYS* 1.3 79.3 - - - +
1004C PHE* 1.3 65.2 + - - -
30F C 5.4 1.7 - - - -
31F T 5.4 1.5 + - - +
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Residues in contact with PHE1004 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
999C ARG* 2.6 58.1 - - + +
1001C SER* 2.6 26.0 + - - +
1003C THR* 1.3 81.4 + - - +
1005C GLU* 1.3 62.8 + - - +
1006C LEU 3.5 1.1 - - - -
1007C GLU* 3.3 27.8 + - - +
1008C ASP* 2.7 30.3 + - - +
30F C 5.5 8.5 - - - -
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Residues in contact with GLU1005 (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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681C PHE* 4.3 5.1 - - + -
994C ARG* 2.2 61.3 + - + +
998C ALA* 3.9 22.6 - - + +
999C ARG 4.7 9.4 - - - +
1000C GLN* 5.5 1.0 - - - -
1001C SER 2.5 20.3 + - - +
1002C LYS* 3.5 27.1 + - - +
1004C PHE* 1.3 71.4 - - - +
1006C LEU* 1.3 70.1 + - + +
1008C ASP* 3.1 5.9 + - - +
1009C ILE* 2.9 28.3 + - + +
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Residues in contact with LEU1006 (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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572C ILE* 4.6 6.1 - - + +
573C SER* 4.6 4.7 - - - -
574C ARG* 3.7 22.0 - - + +
679C LEU* 3.6 52.1 - - + +
680C MET 4.1 2.0 - - - +
681C PHE* 4.2 42.6 - - + +
990C PHE* 4.6 3.1 - - + -
1002C LYS 4.2 8.7 + - - +
1005C GLU* 1.3 85.1 - - + +
1007C GLU* 1.3 64.1 + - - +
1009C ILE* 4.2 18.8 - - + +
1010C LEU* 2.8 28.4 + - - +
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Residues in contact with GLU1007 (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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553C ILE* 3.8 38.5 - - + +
555C ASP* 5.6 0.3 - - - +
574C ARG* 3.6 34.2 + - - +
999C ARG* 5.6 0.6 + - - -
1004C PHE* 3.3 33.8 + - - +
1005C GLU 3.2 0.6 - - - -
1006C LEU* 1.3 77.6 - - - +
1008C ASP* 1.3 67.8 + - - +
1010C LEU* 3.4 2.5 + - - +
1011C LYS* 3.0 24.2 + - + +
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Residues in contact with ASP1008 (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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997C ASN* 4.0 16.6 - - + +
999C ARG* 2.1 53.8 + - - +
1004C PHE* 2.7 18.7 + - - +
1005C GLU* 3.6 5.8 - - - +
1007C GLU* 1.3 84.5 - - - +
1009C ILE* 1.3 63.6 + - - +
1011C LYS* 3.1 15.3 + - - +
1012C HIS* 3.0 28.8 + - + +
23E G 3.8 12.5 - - - +
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Residues in contact with ILE1009 (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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679C LEU* 3.9 22.4 - - + -
990C PHE* 4.4 17.0 - - + +
993C PHE* 4.1 17.4 - - + +
994C ARG* 3.6 52.7 - - + +
997C ASN* 5.5 3.1 - - + -
998C ALA 5.3 5.4 - - - +
1005C GLU* 2.9 22.3 + - + +
1006C LEU* 3.8 17.5 - - + +
1008C ASP* 1.3 75.9 - - - +
1010C LEU* 1.3 65.5 + - - +
1012C HIS* 3.2 5.4 + - - +
1013C HIS* 2.9 26.7 + - + +
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Residues in contact with LEU1010 (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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553C ILE* 4.6 11.2 - - + -
574C ARG* 4.6 3.8 - - + -
575C ARG* 4.4 21.1 - - - +
576C PHE* 3.4 49.6 - - + -
676C PRO* 3.9 24.5 - - + +
677C LEU 4.7 2.0 - - - +
679C LEU* 3.8 27.4 - - + -
1006C LEU 2.8 20.9 + - - +
1007C GLU 3.8 1.8 - - - +
1009C ILE* 1.3 75.8 - - - +
1011C LYS* 1.3 64.9 + - - +
1013C HIS* 4.4 2.9 - - - -
1014C TRP* 2.9 24.6 + - + +
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Residues in contact with LYS1011 (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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490C ARG* 4.9 12.5 - - - +
523C ARG* 5.4 9.3 - - - +
526C GLU* 4.2 7.7 + - - +
530C LEU* 3.7 37.7 - - + +
553C ILE* 4.4 12.5 - - + +
576C PHE* 5.9 0.9 - - - -
1007C GLU* 3.0 15.9 + - - +
1008C ASP* 3.1 17.0 + - - +
1010C LEU* 1.3 78.0 - - - +
1012C HIS* 1.3 70.4 + - + +
1014C TRP* 3.8 2.5 - - - +
1015C LEU* 3.1 34.7 + - + +
23E G 4.5 8.7 + - - -
24E C 4.0 27.9 + - - -
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Residues in contact with HIS1012 (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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490C ARG* 2.7 37.0 + - - -
491C VAL* 3.9 24.2 - - + +
495C LEU 5.4 2.0 + - - -
497C CYS* 5.4 0.2 - - - -
993C PHE* 3.4 23.3 - + + -
997C ASN* 3.0 44.8 + - + +
1008C ASP* 3.0 17.7 + - + +
1009C ILE* 3.8 2.5 - - - +
1011C LYS* 1.3 86.7 + - + +
1013C HIS* 1.3 57.1 + - - +
1015C LEU* 3.2 12.4 + - + +
1016C TYR* 2.9 26.5 + - - +
23E G 3.8 11.2 - - - -
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Residues in contact with HIS1013 (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* 4.9 17.1 - - - -
671C GLU* 5.7 1.6 - - + -
674C CYS 4.1 11.7 - - - -
676C PRO* 3.2 40.4 - - + +
679C LEU* 6.5 0.7 - - + -
986C GLY* 4.3 6.7 + - - -
989C LEU* 3.4 42.6 - - + +
990C PHE* 4.6 9.4 + + + -
993C PHE* 3.3 18.5 - + + -
1009C ILE* 2.9 20.9 + - + +
1010C LEU* 3.8 4.9 - - - +
1012C HIS* 1.3 77.0 - - - +
1014C TRP* 1.3 54.7 + - - +
1016C TYR* 2.6 27.2 + + - +
1017C THR* 3.0 16.3 + - + +
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Residues in contact with TRP1014 (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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529C LEU* 3.1 20.7 + - - +
530C LEU* 3.4 31.3 - - + +
531C PRO* 3.6 9.8 - - + +
576C PHE* 4.4 16.8 - + + -
581C ALA* 3.6 24.5 - - + -
584C SER* 3.1 25.1 - - - -
585C ALA* 4.2 0.4 - - + -
644C PHE* 4.7 6.5 - + - -
675C ARG* 1.3 99.1 + - + -
676C PRO* 4.1 19.4 - - + +
1010C LEU 2.9 17.3 + - - +
1011C LYS 3.8 1.8 - - - +
1013C HIS* 1.3 75.9 + - - +
1015C LEU* 1.3 65.7 + - + +
1017C THR* 3.3 19.9 + - - +
1018C SER* 3.8 9.9 + - - -
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Residues in contact with LEU1015 (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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487C LEU* 3.9 26.7 - - + -
490C ARG* 5.9 1.1 - - - +
491C VAL* 3.7 27.4 - - + -
526C GLU* 4.2 15.0 - - + +
529C LEU* 4.5 19.1 - - + -
530C LEU* 3.7 23.1 - - + -
1011C LYS* 3.1 23.8 + - + +
1012C HIS* 3.3 17.0 - - + +
1014C TRP* 1.3 83.4 - - + +
1016C TYR* 1.3 62.0 + - - +
1017C THR 3.1 1.4 + - - -
1018C SER* 3.5 10.8 + - - -
1021C LEU* 3.4 25.4 - - + +
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Residues in contact with TYR1016 (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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502A LYS* 6.0 0.3 + - - -
491C VAL* 3.6 24.7 - - + +
492C ASN* 3.3 35.6 + - - -
494C PHE* 6.0 5.4 - + - -
671C GLU* 5.2 3.4 - - + -
672C LEU* 3.5 32.9 - - + +
989C LEU* 3.4 48.9 - - + +
993C PHE* 4.3 8.1 - + + -
1012C HIS 2.9 11.4 + - - +
1013C HIS* 2.6 22.3 + + - +
1015C LEU* 1.3 72.0 - - - +
1017C THR* 1.3 58.2 + - - -
1018C SER 3.5 0.7 - - - -
1021C LEU* 6.0 1.1 - - - -
1022C GLN* 2.8 18.2 + - + +
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Residues in contact with THR1017 (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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671C GLU 4.8 3.1 - - - -
672C LEU 3.7 6.4 + - - +
673C SER* 4.2 2.1 - - - -
674C CYS 3.5 27.4 + - - -
675C ARG* 2.9 35.8 - - - +
676C PRO* 3.6 22.9 - - + -
1013C HIS* 3.3 18.4 - - - +
1014C TRP* 3.3 11.0 - - - +
1015C LEU 3.1 0.2 - - - -
1016C TYR* 1.3 80.9 - - - +
1018C SER* 1.3 55.9 + - - +
1019C LYS 3.7 1.9 + - - -
1022C GLN* 3.1 12.5 + - - +
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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