Contacts of the helix formed by residues 634 - 643 (chain A) in PDB entry 2MPF
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 SER 634 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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559A LYS* 3.1 13.3 + - - +
578A GLY 6.0 0.9 - - - -
580A LYS* 3.8 23.5 - - - +
633A LEU* 1.3 82.7 - - - +
635A VAL* 1.3 66.4 + - - +
636A ASP* 3.2 9.4 - - - -
637A ASN* 2.8 38.6 + - - -
638A PHE* 3.5 3.5 + - - +
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Residues in contact with VAL 635 (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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578A GLY* 3.9 17.8 + - - +
579A LYS 3.7 20.6 + - - +
580A LYS* 4.1 8.8 - - - +
581A MET* 5.0 4.5 - - + +
610A ILE* 4.5 14.8 - - + +
611A CYS 5.5 0.2 - - - +
612A LEU* 3.0 57.8 - - + +
633A LEU 3.5 3.9 + - - -
634A SER* 1.3 71.4 - - - +
636A ASP* 1.3 78.4 + - - +
638A PHE* 3.1 6.1 + - + -
639A ASN* 3.0 20.7 + - - +
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Residues in contact with ASP 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A GLY* 4.2 11.7 - - - +
634A SER* 3.2 7.9 + - - -
635A VAL* 1.3 92.3 + - - +
637A ASN* 1.3 62.3 + - - +
639A ASN* 3.3 16.3 + - - +
640A GLU* 2.9 28.5 + - - +
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Residues in contact with ASN 637 (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 MET* 5.5 0.2 - - - +
559A LYS* 3.0 27.8 + - + +
633A LEU* 3.6 24.1 - - + +
634A SER* 2.8 20.8 + - - +
636A ASP* 1.3 78.3 - - - +
638A PHE* 1.3 58.0 + - - +
640A GLU* 3.5 22.0 + - - +
641A VAL* 3.3 23.2 + - - +
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Residues in contact with PHE 638 (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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542A MET* 5.6 4.3 - - + -
545A PHE* 3.6 37.7 - + - -
552A PHE* 3.8 16.6 - + - -
556A MET* 3.4 23.6 - - + -
581A MET* 4.2 23.3 - - + -
612A LEU* 3.5 31.9 - - + -
633A LEU* 4.3 5.3 - - + +
634A SER 3.5 7.5 + - - +
635A VAL* 3.1 10.9 + - + +
637A ASN* 1.3 75.4 - - - +
639A ASN* 1.3 58.6 + - - +
641A VAL* 3.2 11.2 - - - +
642A LEU* 3.0 31.6 + - + +
652A PHE* 3.7 25.1 - + - -
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Residues in contact with ASN 639 (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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612A LEU* 2.9 54.1 + - - +
613A LEU* 4.8 6.2 - - - +
635A VAL* 3.0 14.1 + - - +
636A ASP* 3.3 19.4 + - - +
638A PHE* 1.3 76.0 - - - +
640A GLU* 1.3 57.9 + - - +
642A LEU* 3.8 20.1 - - - +
643A GLU* 3.7 20.7 - - - +
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Residues in contact with GLU 640 (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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636A ASP 2.9 15.4 + - - +
637A ASN* 3.5 27.7 + - - +
638A PHE 3.2 0.4 - - - -
639A ASN* 1.3 76.4 - - - +
641A VAL* 1.3 61.3 + - - +
643A GLU* 3.4 31.5 + - - +
644A GLU* 4.2 5.7 + - - +
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Residues in contact with VAL 641 (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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552A PHE* 4.0 16.6 - - + +
555A ALA* 3.9 30.7 - - + +
556A MET* 4.0 31.2 - - + +
637A ASN 3.3 13.7 - - - +
638A PHE* 3.2 22.7 - - - +
640A GLU* 1.3 73.8 - - - +
642A LEU* 1.3 65.1 + - - +
643A GLU 3.2 1.6 - - - -
644A GLU* 3.1 19.6 + - + +
645A TYR* 3.4 16.4 - - + -
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Residues in contact with LEU 642 (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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552A PHE* 3.6 30.2 - - + -
612A LEU* 4.9 2.2 - - + -
613A LEU* 5.6 1.1 - - + -
638A PHE* 3.0 28.7 + - + +
639A ASN* 3.8 24.2 - - - +
641A VAL* 1.3 76.9 - - - +
643A GLU* 1.3 56.1 + - - +
645A TYR 3.1 30.5 + - - +
648A MET* 3.8 22.9 - - + -
649A ARG* 3.7 21.6 - - + +
652A PHE* 3.7 41.7 - - + -
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Residues in contact with GLU 643 (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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639A ASN 3.7 18.2 - - - +
640A GLU* 3.4 20.2 + - - +
641A VAL 3.2 1.4 - - - -
642A LEU* 1.3 75.0 - - - +
644A GLU* 1.3 59.6 + - + +
645A TYR 3.3 0.6 + - - -
646A PRO* 4.0 11.5 - - - +
649A ARG* 4.0 30.8 + - + +
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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