Contacts of the helix formed by residues 717 - 729 (chain A) in PDB entry 4MVY
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 LEU 717 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575A ASP* 3.0 47.6 - - + +
576A ALA 4.6 0.2 - - - +
579A TYR* 3.9 18.2 - - + -
606A LEU* 4.5 11.9 - - + -
610A LEU* 4.0 27.6 - - + -
713A LEU* 2.9 30.8 + - + +
714A SER 3.5 2.9 - - - -
716A ILE* 1.3 83.9 - - + +
718A PRO* 1.3 58.4 - - - +
720A LYS* 4.1 8.7 - - + -
721A SER* 2.8 31.0 + - - +
724A ILE* 5.8 1.3 - - + -
762A PHE* 4.6 12.6 - - + -
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Residues in contact with PRO 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ARG* 3.3 42.6 - - - +
323A ASP* 5.2 1.3 - - - +
575A ASP* 3.6 13.5 - - - +
578A LYS* 4.7 13.7 - - + +
714A SER* 3.1 15.5 - - - +
715A PRO 4.2 4.3 - - - +
716A ILE 3.3 10.5 - - - +
717A LEU* 1.3 88.2 - - - +
719A ARG* 1.3 67.0 + - + +
721A SER* 3.1 15.0 + - - +
722A VAL* 3.4 15.1 - - - +
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Residues in contact with ARG 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ARG* 6.3 0.2 - - - -
323A ASP* 2.7 41.9 + - - +
574A TYR* 6.2 2.0 - - + -
575A ASP* 2.8 22.6 + - - +
718A PRO* 1.3 78.3 - - + +
720A LYS* 1.3 66.6 + - + +
722A VAL* 3.3 19.1 + - - +
723A VAL* 3.3 16.0 + - - +
803A GOL 3.1 48.3 + - - -
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Residues in contact with LYS 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A GLY* 6.5 1.3 - - - -
575A ASP* 2.8 31.5 + - + +
717A LEU* 4.1 8.5 - - + -
719A ARG* 1.3 74.1 - - + +
721A SER* 1.3 59.7 + - - +
723A VAL* 3.2 11.7 + - + +
724A ILE* 3.0 36.8 + - + +
760A VAL 5.1 2.0 + - - -
761A LEU* 2.9 38.9 + - + +
762A PHE* 3.7 35.6 - - + -
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Residues in contact with SER 721 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A THR* 3.8 21.9 - - - +
713A LEU* 5.1 0.4 - - - -
714A SER* 3.3 34.3 - - - -
717A LEU* 2.8 19.7 + - - +
718A PRO* 3.1 14.4 + - - +
720A LYS* 1.3 76.0 - - - +
722A VAL* 1.3 62.2 + - - +
724A ILE* 3.5 3.8 + - - +
725A PHE* 2.9 39.6 + - - -
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Residues in contact with VAL 722 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718A PRO 3.4 16.2 - - - +
719A ARG* 3.3 14.0 + - - +
720A LYS 3.2 0.4 - - - -
721A SER* 1.3 77.6 + - - +
723A VAL* 1.3 61.0 + - + +
725A PHE* 3.8 4.7 - - + +
726A ASP* 2.8 40.8 + - - +
735A ARG* 3.8 21.5 - - - +
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Residues in contact with VAL 723 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A ARG 3.3 13.9 + - - +
720A LYS* 3.2 16.7 + - + +
722A VAL* 1.3 77.5 - - + +
724A ILE* 1.3 57.5 + - - +
726A ASP* 3.3 9.4 + - - +
727A MET* 2.9 46.8 + - + +
761A LEU* 3.4 25.6 - - + -
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Residues in contact with ILE 724 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A LEU* 4.1 22.9 - - + -
614A VAL* 4.1 17.9 - - + -
706A VAL* 4.1 0.7 - - + -
710A THR* 3.6 36.6 - - + +
717A LEU* 5.8 2.0 - - + -
720A LYS* 3.0 26.7 + - + +
721A SER* 3.6 4.7 - - - +
723A VAL* 1.3 75.6 - - - +
725A PHE* 1.3 64.3 + - - +
727A MET* 3.0 12.3 + - - +
728A LEU* 2.9 38.2 + - + +
761A LEU* 3.6 31.9 - - + -
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Residues in contact with PHE 725 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707A ARG* 3.7 30.1 - - + -
710A THR* 3.9 13.0 - - + -
711A LEU* 3.7 35.4 - - + -
714A SER* 4.9 3.8 - - - -
721A SER* 2.9 36.4 + - - +
722A VAL* 3.8 5.4 - - + +
724A ILE* 1.3 73.8 - - - +
726A ASP* 1.3 56.2 + - - +
728A LEU* 3.2 4.5 + - + -
729A GLY 2.9 23.6 + - - -
730A VAL* 2.9 34.4 + - + -
734A HIS 5.3 1.3 - - - -
735A ARG* 3.4 56.9 + - + +
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Residues in contact with ASP 726 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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722A VAL* 2.8 34.0 + - - +
723A VAL* 3.4 8.2 - - - +
725A PHE* 1.3 70.3 - - - +
727A MET* 1.3 66.4 + - + +
729A GLY* 3.0 12.3 + - - -
735A ARG* 2.7 38.1 + - - +
753A GLY* 3.3 16.3 - - - -
754A PRO* 5.1 1.0 - - - +
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Residues in contact with MET 727 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A VAL* 3.8 23.3 - - + -
615A MET* 4.7 14.8 - - - +
618A THR* 4.1 18.3 - - + +
723A VAL* 2.9 39.3 + - + +
724A ILE* 3.0 9.6 + - - +
726A ASP* 1.3 75.8 - - + +
728A LEU* 1.3 61.2 + - + +
729A GLY 3.2 0.2 - - - -
752A LEU* 3.6 10.6 - - - +
753A GLY* 3.1 24.2 + - - +
754A PRO 5.5 4.5 - - - +
759A GLU* 3.0 38.6 - - + +
760A VAL 5.3 0.9 - - - -
761A LEU* 4.2 16.2 - - + +
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Residues in contact with LEU 728 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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614A VAL* 4.6 6.1 - - + -
617A CYS* 4.5 7.6 - - - -
618A THR* 3.6 24.5 - - + -
628A TRP* 2.9 32.5 + - + -
703A LEU* 4.2 23.8 - - + +
706A VAL* 3.8 26.2 - - + -
707A ARG* 4.1 22.9 - - + +
724A ILE* 2.9 25.8 + - + +
725A PHE* 3.7 6.1 - - + +
726A ASP 3.2 0.2 - - - -
727A MET* 1.3 77.4 - - + +
729A GLY* 1.3 60.0 + - - +
730A VAL* 3.8 13.5 - - + -
751A ARG 3.9 0.7 - - - +
752A LEU* 3.4 11.8 - - - +
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Residues in contact with GLY 729 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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725A PHE 2.9 5.8 + - - -
726A ASP* 3.0 12.8 + - - -
727A MET 3.2 1.0 + - - -
728A LEU* 1.3 78.9 - - - +
730A VAL* 1.3 63.3 + - - +
731A PRO* 3.3 3.5 - - - +
735A ARG* 5.5 0.2 - - - -
750A THR* 3.3 22.9 - - - +
751A ARG 3.4 14.9 - - - +
752A LEU 4.2 0.2 - - - -
753A GLY* 3.8 5.8 - - - -
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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