Contacts of the helix formed by residues 582 - 591 (chain A) in PDB entry 1M2V
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 582 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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525A GLN* 2.6 33.8 + - + +
526A GLU* 5.7 5.2 - - + +
578A PRO 5.2 0.2 - - - +
581A SER* 1.3 80.1 + - - +
583A TYR* 1.3 64.0 + - - +
584A PRO* 3.3 3.6 - - - -
585A GLN* 2.9 46.1 + - - +
586A PHE* 3.0 34.2 + - + -
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Residues in contact with TYR 583 (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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31A VAL* 4.3 7.1 - - + +
523A PHE* 4.3 7.4 - + + -
525A GLN* 3.0 30.6 + - + -
528A ALA* 3.9 13.7 - - + -
529A ALA* 3.7 29.6 - - + -
532A MET* 3.2 33.8 - - + +
552A LEU* 5.4 3.5 + - - +
555A THR* 4.9 3.3 + - - -
556A LEU* 3.3 34.8 - - + -
559A LEU* 3.7 23.1 - - + -
560A CYS* 6.0 0.2 - - - -
580A PHE* 3.1 8.9 + - + +
582A LEU* 1.3 73.9 - - - +
584A PRO* 1.4 56.1 - - + +
586A PHE* 3.0 11.8 + - - +
587A THR* 2.8 52.5 + - - -
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Residues in contact with PRO 584 (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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556A LEU* 3.7 22.2 - - + -
560A CYS* 4.5 2.0 - - - -
576A LEU* 3.8 25.1 - - + -
580A PHE 3.2 13.2 - - - +
581A SER 3.8 6.5 - - - +
582A LEU 3.3 4.0 - - - -
583A TYR* 1.4 93.1 - - + +
585A GLN* 1.3 56.1 + - - +
587A THR* 3.3 2.8 + - - -
588A TYR* 2.8 29.2 + - - +
755A PHE* 3.6 5.6 - - - -
756A MET* 3.9 19.3 - - + -
759A LEU* 3.8 24.0 - - + -
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Residues in contact with GLN 585 (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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581A SER 4.9 2.4 + - - +
582A LEU* 2.9 38.5 + - - +
584A PRO* 1.3 77.6 - - - +
586A PHE* 1.3 68.3 + - - +
588A TYR* 3.1 4.9 + - - +
589A TYR* 2.9 28.9 + - + -
626A GLN* 3.1 37.4 + - - +
752A LEU* 3.9 37.6 - - + +
756A MET* 5.1 3.0 - - + +
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Residues in contact with PHE 586 (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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525A GLN 4.1 10.8 - - - -
526A GLU* 4.3 17.7 - - + -
529A ALA* 3.7 28.9 - - + -
582A LEU* 3.0 49.7 + - + -
583A TYR* 3.0 11.5 + - - +
585A GLN* 1.3 78.1 - - - +
587A THR* 1.3 57.3 + - - +
589A TYR* 3.4 1.7 + - - +
590A LEU* 2.8 31.7 + - - +
622A LEU* 3.6 34.1 - - + -
625A ILE* 3.3 11.1 - - + +
626A GLN* 3.7 37.5 - - + -
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Residues in contact with THR 587 (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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529A ALA* 5.6 0.2 - - - +
552A LEU* 4.3 28.7 - - + +
553A ASP* 4.6 1.1 - - - +
556A LEU* 3.6 24.2 - - + +
583A TYR* 2.8 41.9 + - - +
584A PRO 3.4 8.3 - - - -
586A PHE* 1.3 75.2 - - - +
588A TYR* 1.3 64.1 + - - +
590A LEU* 3.0 10.0 + - - +
591A ARG* 2.9 43.5 + - - +
755A PHE* 4.3 0.2 - - + -
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Residues in contact with TYR 588 (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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584A PRO 2.8 14.7 + - - +
585A GLN 3.1 7.4 + - - +
587A THR* 1.3 75.6 - - - +
589A TYR* 1.3 97.0 + + - +
591A ARG* 3.1 29.1 + - - +
592A ARG* 3.6 34.0 + - + +
750A VAL 3.2 28.0 + - - -
751A SER* 3.8 4.2 - - - -
752A LEU* 3.5 45.7 + - + -
755A PHE* 3.7 30.7 - + + -
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Residues in contact with TYR 589 (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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585A GLN* 2.9 27.7 + - + +
586A PHE 3.9 3.4 - - - +
588A TYR* 1.3 96.4 - + - +
590A LEU* 1.3 65.2 + - - +
592A ARG* 3.1 48.3 + - - +
593A SER* 3.1 13.9 + - - -
625A ILE* 3.6 24.5 - - + +
626A GLN* 2.9 44.6 - - + -
627A PRO* 5.1 3.1 - - + -
643A LEU* 3.5 37.0 + - + +
752A LEU* 4.7 9.9 - - + +
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Residues in contact with LEU 590 (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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529A ALA* 4.7 5.6 - - + +
532A MET* 4.8 1.8 - - + -
533A ALA* 3.5 42.0 - - + +
552A LEU* 3.6 30.3 - - + -
586A PHE 2.8 22.0 + - - +
587A THR* 3.5 6.5 - - - +
589A TYR* 1.3 71.4 - - - +
591A ARG* 1.3 60.9 + - - +
592A ARG 2.8 5.0 + - - -
593A SER* 2.6 25.8 + - - -
595A PHE* 3.8 21.3 - - + -
596A LEU* 3.7 21.5 - - + +
625A ILE* 3.4 16.7 - - + +
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Residues in contact with ARG 591 (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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549A ILE* 3.4 36.8 - - + +
552A LEU* 4.7 6.5 - - + +
553A ASP* 2.8 41.0 + - - -
587A THR* 2.9 37.7 + - - +
588A TYR* 3.1 19.2 + - - +
590A LEU* 1.3 77.4 - - - +
592A ARG* 1.3 51.7 + - - +
593A SER 3.6 0.2 - - - -
596A LEU* 4.3 11.8 - - - +
597A SER* 2.7 27.4 + - - -
755A PHE* 3.5 30.4 - - - -
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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