Contacts of the helix formed by residues 717 - 725 (chain D) in PDB entry 1MVW
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 TYR 717 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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715D VAL 3.5 1.4 + - - -
716D LEU* 1.3 75.8 - - + +
718D ALA* 1.3 57.0 + - - +
720D PHE* 2.9 7.5 + - + +
721D LYS* 2.8 24.3 + - - +
740D SER* 3.5 18.1 - - - +
741D LYS* 3.9 42.0 - - + +
744D SER* 2.9 37.6 + - - -
760D PHE* 3.1 37.7 - + - +
761D GLY 3.3 24.6 + - - -
762D HIS 4.8 1.1 - - - -
763D THR* 3.6 20.4 - - - +
764D MLY 3.6 5.4 - - - -
765D VAL* 3.4 26.2 - - + +
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Residues in contact with ALA 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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716D LEU* 3.5 7.9 - - + +
717D TYR* 1.3 71.3 - - - +
719D ASP* 1.4 60.9 - - - +
720D PHE 2.8 5.5 + - - -
721D LYS* 2.8 27.3 + - + +
722D GLN* 3.0 19.8 + - - +
740D SER* 4.3 15.0 + - - +
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Residues in contact with ASP 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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715D VAL* 4.1 5.4 - - + +
716D LEU* 3.2 38.6 - - + +
718D ALA* 1.4 81.6 - - - +
720D PHE* 1.4 57.0 + - - +
722D GLN* 4.8 4.1 - - - +
723D ARG* 3.7 21.4 + - - +
724D TYR* 4.9 1.7 - - - -
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Residues in contact with PHE 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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715D VAL* 3.3 32.3 - - + +
716D LEU 2.8 4.2 + - - +
717D TYR* 3.0 17.5 - + + +
718D ALA 2.8 0.2 - - - -
719D ASP* 1.4 80.7 - - - +
721D LYS* 1.3 65.8 + - - +
723D ARG 4.4 0.2 - - - -
724D TYR* 3.4 46.9 + + + +
736D GLN* 3.4 4.5 + - - -
744D SER* 3.3 25.8 - - - +
747D LEU* 4.8 11.0 - - + -
748D LEU* 3.6 35.7 - - + -
765D VAL* 5.5 3.1 - - + -
767D PHE* 3.5 27.4 - + - -
778D MET* 4.9 7.0 - - - -
782D MLY 6.3 0.2 - - - -
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Residues in contact with LYS 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 TYR 2.8 8.3 + - - +
718D ALA* 2.8 13.2 + - + +
720D PHE* 1.3 73.6 - - - +
722D GLN* 1.3 61.9 + - - +
724D TYR 2.9 3.6 + - - -
725D ARG* 2.7 21.1 + - - +
733D PRO 3.9 0.4 - - - -
736D GLN* 0.8 219.4 + - + +
737D PHE* 2.1 28.0 + - + +
740D SER* 4.0 14.5 - - - +
743D ALA* 3.9 1.8 - - + -
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Residues in contact with GLN 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 ALA 3.0 10.4 + - - +
719D ASP* 5.2 3.4 - - - +
721D LYS* 1.3 80.7 - - - +
723D ARG* 1.3 72.2 + - + +
724D TYR 3.3 0.5 + - - -
725D ARG* 3.9 9.9 + - - +
726D VAL* 4.9 6.4 - - - +
736D GLN* 4.2 0.9 - - - -
786D ILE* 5.9 1.7 - - - +
93F VAL* 4.3 21.1 - - - +
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Residues in contact with ARG 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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719D ASP 3.7 15.2 + - - +
720D PHE 4.1 0.4 + - - -
721D LYS 3.3 0.8 - - - -
722D GLN* 1.3 85.1 - - + +
724D TYR* 1.3 82.7 + - + +
726D VAL* 5.2 2.6 - - - +
779D ARG* 2.2 68.5 - - - +
782D MLY 3.3 20.8 - - - +
783D LEU* 3.9 21.8 - - - +
786D ILE* 5.2 10.0 - - - +
93F VAL* 6.3 1.2 - - - +
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Residues in contact with TYR 724 (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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715D VAL* 5.7 4.9 - - + -
719D ASP 5.0 2.5 - - - -
720D PHE* 3.5 47.6 - + + +
721D LYS 2.9 2.6 + - - -
723D ARG* 1.3 91.0 - - + +
725D ARG* 1.3 51.4 - - - +
726D VAL 3.0 1.6 - - - -
727D LEU* 3.1 8.3 - - + -
775D LEU* 3.3 15.7 + - + +
778D MET* 2.9 39.2 - - + +
779D ARG* 2.9 29.8 + - + +
782D MLY 1.2 134.3 + - + +
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Residues in contact with ARG 725 (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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721D LYS 2.7 19.8 + - - +
722D GLN* 3.9 7.6 + - - +
723D ARG 3.9 0.4 - - - -
724D TYR* 1.3 69.7 - - - +
726D VAL* 1.3 55.2 + - + +
727D LEU 2.8 12.0 + - - -
729D ALA* 2.9 22.4 + - - +
732D ILE* 3.3 8.7 - - - +
733D PRO* 2.0 60.7 - - + +
734D GLU* 6.1 0.2 - - - +
736D GLN* 3.5 6.7 - - - +
737D PHE* 2.7 32.3 - - - -
782D MLY 2.7 12.7 - - - -
86F ASP* 4.9 11.1 + - - -
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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