Contacts of the helix formed by residues 708 - 723 (chain D) in PDB entry 1V40
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 LYS 708 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706D GLU* 2.7 44.5 + - - +
707D LYS* 1.3 74.1 - - + +
709D GLN* 1.3 62.7 + - - +
710D ASP* 3.4 11.0 - - - +
711D VAL* 2.9 42.7 - - + +
712D LYS* 3.1 6.1 + - - +
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Residues in contact with GLN 709 (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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706D GLU 3.7 12.5 + - - -
707D LYS* 3.1 23.4 + - - +
708D LYS* 1.3 71.3 - - - +
710D ASP* 1.3 58.4 + - - +
712D LYS* 3.6 22.2 + - - +
713D GLU* 2.9 36.0 + - - +
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Residues in contact with ASP 710 (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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708D LYS* 3.6 18.7 - - - +
709D GLN* 1.3 74.6 + - - +
711D VAL* 1.3 67.5 + - - +
713D GLU* 3.9 4.6 - - - +
714D GLN* 3.0 29.2 + - - +
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Residues in contact with VAL 711 (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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706D GLU* 3.3 20.6 - - + +
708D LYS* 2.9 52.9 - - + +
710D ASP* 1.3 81.4 + - - +
712D LYS* 1.3 69.3 + - - +
714D GLN* 3.3 6.3 + - + +
715D MET* 3.0 30.0 + - + +
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Residues in contact with LYS 712 (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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703D PRO* 3.7 28.3 - - - +
704D TRP* 3.6 18.2 + - - +
706D GLU* 3.6 28.7 + - + +
708D LYS 3.1 13.6 + - - +
709D GLN* 3.6 22.9 + - - +
711D VAL* 1.3 81.6 - - - +
713D GLU* 1.3 58.9 + - - +
715D MET* 3.1 4.3 + - - +
716D PHE* 2.9 57.6 + - + -
763D PHE* 6.2 1.8 - - - -
799D LEU* 5.9 2.0 - - - +
3801D O16 5.4 13.3 - - - -
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Residues in contact with GLU 713 (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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709D GLN* 2.9 21.0 + - - +
710D ASP* 3.9 4.9 - - - +
712D LYS* 1.3 77.0 - - - +
714D GLN* 1.3 62.8 + - - +
716D PHE* 3.3 7.7 + - + +
717D ASN* 3.0 46.3 + - - +
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Residues in contact with GLN 714 (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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710D ASP 3.0 20.5 + - - +
711D VAL* 3.5 8.1 - - + +
712D LYS 3.2 0.2 - - - -
713D GLU* 1.3 77.0 - - - +
715D MET* 1.3 58.2 + - - +
717D ASN* 3.3 10.5 + - - +
718D GLU* 2.8 62.2 + - - +
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Residues in contact with MET 715 (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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701D CYS 4.5 7.4 - - - +
703D PRO* 3.6 38.4 - - + -
711D VAL* 3.0 22.1 + - + +
712D LYS 3.6 3.6 - - - +
714D GLN* 1.3 74.6 - - - +
716D PHE* 1.3 67.2 + - - +
718D GLU* 3.7 15.7 - - + +
719D LEU* 2.9 35.4 + - + +
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Residues in contact with PHE 716 (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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702D PHE* 3.9 26.0 - + + -
703D PRO* 3.5 36.3 - - + -
704D TRP* 3.7 39.3 - + - -
712D LYS* 2.9 45.6 + - + +
713D GLU* 3.5 12.3 - - + +
715D MET* 1.3 78.0 - - - +
717D ASN* 1.3 65.6 + - - +
719D LEU* 3.7 1.4 - - - +
720D LEU* 2.9 33.8 + - + +
763D PHE* 3.8 41.7 - + + -
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Residues in contact with ASN 717 (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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713D GLU* 3.0 43.3 + - - +
714D GLN* 3.7 13.1 - - - +
716D PHE* 1.3 80.1 - - - +
718D GLU* 1.3 57.5 + - + +
720D LEU* 3.8 6.4 - - - +
721D THR* 2.8 38.4 + - - +
763D PHE* 4.8 9.4 - - - +
764D LYS* 6.1 1.5 - - - +
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Residues in contact with GLU 718 (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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714D GLN* 2.8 48.9 + - - +
715D MET* 3.7 16.6 - - + +
716D PHE 3.2 0.2 - - - -
717D ASN* 1.3 77.9 - - + +
719D LEU* 1.3 58.8 + - + +
722D TYR* 2.8 63.9 + - + +
723D ASN* 4.2 2.7 - - - +
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Residues in contact with LEU 719 (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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698D PHE* 3.9 5.4 - - + -
701D CYS* 3.6 41.1 - - + +
702D PHE* 3.8 34.8 - - + -
715D MET* 2.9 35.2 + - + +
716D PHE 3.7 3.1 - - - +
718D GLU* 1.3 77.1 - - + +
720D LEU* 1.3 58.9 + - - +
723D ASN* 3.0 33.4 + - + +
724D ALA* 2.8 27.5 + - - +
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Residues in contact with LEU 720 (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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698D PHE* 4.7 0.4 - - + -
702D PHE* 3.2 38.8 - - + -
716D PHE* 2.9 30.4 + - + +
717D ASN* 3.9 7.6 - - - +
719D LEU* 1.3 77.4 - - - +
721D THR* 1.3 60.9 + - - +
724D ALA* 3.5 24.2 - - + +
725D PRO* 3.6 6.8 - - - +
760D LEU* 4.4 14.6 - - + +
763D PHE* 3.7 35.2 - - + +
764D LYS* 3.7 40.8 - - + +
767D LEU* 5.0 1.9 - - + +
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Residues in contact with THR 721 (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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717D ASN* 2.8 23.6 + - - +
718D GLU* 4.1 2.0 - - - -
720D LEU* 1.3 79.8 - - - +
722D TYR* 1.3 81.4 + - + +
725D PRO* 3.2 20.4 - - - +
764D LYS* 3.1 26.1 + - - +
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Residues in contact with TYR 722 (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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718D GLU* 2.8 53.6 + - + +
721D THR* 1.3 96.1 - - + +
723D ASN* 1.3 67.6 + - - +
725D PRO* 4.0 1.5 - - - +
726D HIS* 3.2 26.3 + - - -
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Residues in contact with ASN 723 (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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3001A GOL 4.5 2.9 + - - -
698D PHE* 3.9 17.7 - - + -
718D GLU* 3.7 5.1 + - - +
719D LEU* 3.0 40.7 + - + +
722D TYR* 1.3 85.8 - - - +
724D ALA* 1.3 66.6 + - - +
725D PRO* 3.3 2.9 - - - -
726D HIS* 3.2 22.6 + - - +
727D LEU* 3.7 5.0 + - - +
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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