Contacts of the helix formed by residues 688 - 703 (chain D) in PDB entry 6VVT
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 HIS 688 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D VAL* 4.8 0.4 - - - -
586D TYR* 3.8 15.7 - + - -
686D GLN* 3.0 59.3 + - + +
687D MET* 1.3 76.3 - - - +
689D LYS* 1.3 58.5 + - - +
690D LYS* 3.2 9.6 - - + +
691D VAL* 3.5 16.9 - - + +
692D GLN* 2.7 38.7 + - - +
803D LYS* 3.5 19.5 + - + -
804D SER 3.7 8.5 - - - +
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Residues in contact with LYS 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576D MET* 3.7 24.2 - - - +
577D PRO 3.7 18.4 - - - +
578D ARG* 4.2 14.9 - - - +
582D VAL* 3.8 15.0 - - + +
688D HIS* 1.3 72.2 - - - +
690D LYS* 1.3 52.9 + - - +
692D GLN* 3.4 6.1 - - + +
693D ALA* 2.4 39.5 + - + +
804D SER 3.1 16.7 + - - +
805D GLY* 3.2 27.8 + - - +
806D ALA 4.2 8.1 + - - -
807D THR 5.8 0.6 - - - -
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Residues in contact with LYS 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688D HIS* 3.2 6.3 - - + +
689D LYS* 1.3 78.7 - - - +
691D VAL* 1.3 53.9 + - + +
693D ALA* 3.2 8.0 - - - +
694D ARG* 2.1 43.3 + - + +
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Residues in contact with VAL 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685D GLU* 4.1 22.4 - - - +
686D GLN 4.3 8.3 - - - +
687D MET* 3.5 35.9 - - + -
688D HIS* 3.2 28.1 + - + +
690D LYS* 1.3 78.1 - - + +
692D GLN* 1.3 52.7 + - - +
694D ARG* 3.4 12.0 - - - +
695D ILE* 2.5 47.3 + - + +
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Residues in contact with GLN 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576D MET* 4.8 7.6 - - + -
577D PRO* 4.0 22.2 + - - +
581D MET 4.8 1.2 + - - -
582D VAL* 4.0 17.2 - - - +
585D LEU* 3.2 37.4 - - - +
672D PHE* 5.1 2.7 - - + -
687D MET* 3.6 37.9 - - + +
688D HIS 2.7 27.2 + - - +
689D LYS* 3.7 5.6 - - - +
691D VAL* 1.3 71.7 - - - +
693D ALA* 1.3 55.7 + - - +
695D ILE* 4.2 5.8 - - - -
696D ILE* 2.8 41.7 + - + +
715D LEU* 4.9 4.6 - - + +
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Residues in contact with ALA 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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573D PRO* 5.6 0.2 - - + -
576D MET* 3.4 30.9 - - + -
689D LYS* 2.4 35.1 + - + +
690D LYS* 3.2 9.4 - - - +
692D GLN* 1.3 67.4 - - - +
694D ARG* 1.3 60.2 + - - +
696D ILE* 4.1 1.2 - - - +
697D ASN* 2.5 41.3 + - - +
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Residues in contact with ARG 694 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680D TYR* 4.0 13.3 + - - -
683D VAL* 5.0 6.5 - - - +
685D GLU* 3.8 21.8 + - - -
690D LYS* 2.1 34.2 + - + +
691D VAL* 3.5 11.1 - - - +
693D ALA* 1.3 67.4 - - - +
695D ILE* 1.3 86.3 + - - +
697D ASN* 3.9 7.1 - - - +
698D ASP* 3.2 33.3 + - - +
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Residues in contact with ILE 695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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672D PHE* 5.8 1.8 - - + -
676D LEU* 4.2 15.9 - - + -
680D TYR* 4.1 13.4 + - - +
683D VAL* 3.7 30.1 - - + -
687D MET* 3.1 35.0 - - + -
691D VAL* 2.5 28.9 + - + +
692D GLN* 3.9 4.9 - - - +
694D ARG* 1.3 88.7 - - - +
696D ILE* 1.3 68.7 + - + +
698D ASP* 3.2 2.9 + - - +
699D LEU* 2.9 44.8 + - + +
715D LEU* 6.4 1.8 - - + -
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Residues in contact with ILE 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D ILE* 5.5 1.3 - - + -
566D LEU* 5.8 0.4 - - + -
573D PRO* 3.8 25.8 - - + -
576D MET* 3.7 17.0 - - + -
577D PRO* 3.5 31.9 - - + -
692D GLN* 2.8 30.9 + - + +
693D ALA 4.2 1.8 - - - +
695D ILE* 1.3 74.4 - - + +
697D ASN* 1.3 53.4 + - - +
699D LEU* 3.2 15.6 - - + +
700D ALA* 2.7 38.5 + - + +
708D VAL* 4.5 18.2 - - + -
711D THR* 6.2 0.4 - - + -
712D VAL* 4.5 15.0 - - + -
715D LEU* 4.5 14.4 - - + -
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Residues in contact with ASN 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D LEU* 5.0 2.8 - - - +
571D GLY 4.7 2.4 - - - +
572D LYS* 4.2 6.8 - - - +
573D PRO* 2.8 34.2 - - - +
693D ALA* 2.5 32.6 + - - +
694D ARG* 3.9 6.5 - - - +
696D ILE* 1.3 75.4 - - - +
698D ASP* 1.3 64.9 + - - +
700D ALA* 2.8 18.6 + - - +
701D GLU* 3.1 22.7 + - - +
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Residues in contact with ASP 698 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680D TYR* 3.9 13.6 + - - +
694D ARG* 3.2 27.9 + - + +
695D ILE* 3.2 5.1 + - - +
697D ASN* 1.3 80.0 - - - +
699D LEU* 1.3 60.8 + - - +
701D GLU* 3.5 20.4 + - - +
702D ARG* 2.8 52.0 + - - +
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Residues in contact with LEU 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676D LEU* 5.1 5.4 - - + -
677D PRO* 5.4 6.7 - - + -
680D TYR* 4.1 20.2 - - + -
695D ILE* 2.9 46.8 + - + +
696D ILE* 3.2 19.3 - - + +
698D ASP* 1.3 74.5 - - - +
700D ALA* 1.3 61.8 + - - +
702D ARG* 3.9 0.7 - - - -
703D PHE* 3.2 42.8 + - + +
707D VAL* 5.6 0.7 - - + -
708D VAL* 3.6 35.5 - - + +
711D THR* 4.6 23.6 - - + +
712D VAL* 5.9 0.4 - - + -
715D LEU* 6.3 0.7 - - + -
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Residues in contact with ALA 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566D LEU* 4.4 26.4 - - + +
696D ILE* 2.7 22.9 + - + +
697D ASN* 2.8 10.5 + - - +
699D LEU* 1.3 75.0 - - - +
701D GLU* 1.3 62.6 + - + +
703D PHE 3.2 14.4 - - - +
705D MET* 5.8 4.7 - - + +
708D VAL* 3.6 21.3 - - + +
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Residues in contact with GLU 701 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697D ASN* 3.1 20.2 + - + +
698D ASP* 3.8 19.4 - - - +
699D LEU 3.3 0.4 - - - -
700D ALA* 1.3 80.6 - - + +
702D ARG* 1.3 64.0 + - + +
703D PHE 3.5 1.3 + - - +
920D PHE* 4.5 13.8 - - + -
944D GLY* 6.3 0.4 - - - -
945D ASP* 4.1 18.3 - - - +
946D PRO* 4.2 21.0 - - - +
980D ARG* 5.3 9.0 - - - +
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Residues in contact with ARG 702 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655D TRP* 5.5 6.1 - - - -
679D SER 5.5 0.6 + - - -
680D TYR* 4.0 17.8 + - - +
681D PRO* 4.0 26.1 - - - +
698D ASP* 2.8 55.9 + - - +
699D LEU* 3.6 1.1 + - - +
701D GLU* 1.3 84.1 - - + +
703D PHE* 1.3 82.6 + - + +
704D PRO* 4.7 1.0 - - - +
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Residues in contact with PHE 703 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677D PRO* 4.0 23.1 - - + -
679D SER* 4.0 34.8 - - - -
680D TYR* 4.2 21.8 - + - -
699D LEU* 3.2 25.5 + - + +
700D ALA 3.2 17.5 - - - +
701D GLU 3.5 1.4 - - - -
702D ARG* 1.3 99.5 - - + +
704D PRO* 1.3 73.4 - - + +
705D MET* 3.7 0.9 + - - +
707D VAL* 3.6 35.2 - - + -
708D VAL* 4.1 3.7 - - + +
25E ALA 5.9 1.6 - - - -
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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