Contacts of the strand formed by residues 628 - 633 (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 CYS 628 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A VAL* 3.3 7.3 - - - +
565A PHE* 2.9 44.2 + - - -
571A ILE* 4.6 0.7 - - - -
586A HIS 3.7 3.8 - - - -
587A GLY* 4.3 10.3 - - - -
588A VAL 4.1 16.2 - - - +
589A VAL* 5.0 2.0 - - - -
624A ALA* 3.5 27.8 - - - -
626A THR* 3.0 6.7 + - + +
627A TYR* 1.3 72.1 - - - +
629A ARG* 1.3 60.6 + - - +
630A LEU* 3.7 32.7 + - + +
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Residues in contact with ARG 629 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A PHE* 3.6 32.3 - - + -
563A GLU 4.1 2.7 - - - -
564A VAL* 3.7 13.7 - - + -
585A GLN* 2.9 47.2 + - - +
586A HIS* 2.8 40.1 + - + +
627A TYR* 5.2 12.3 - - + +
628A CYS* 1.3 70.7 - - - +
630A LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A PHE* 3.7 4.2 - - - -
563A GLU* 2.8 37.8 + - + +
565A PHE* 3.9 20.4 - - + -
571A ILE* 3.8 30.1 - - + -
582A TYR* 5.5 6.5 - - + -
583A PHE 3.4 7.9 - - - +
584A ILE* 3.7 34.5 - - + -
585A GLN* 4.7 0.4 - - - -
589A VAL* 5.1 2.5 - - + -
607A PHE* 3.9 7.4 - - + -
628A CYS* 3.7 32.5 - - + +
629A ARG* 1.3 80.7 - - - +
631A TYR* 1.3 73.1 + - - +
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Residues in contact with TYR 631 (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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534A ASN* 5.0 3.3 + - - -
535A CYS* 3.5 34.1 - - - -
538A LEU* 4.5 2.7 - - + -
560A LEU* 4.0 26.9 - - + -
561A LYS* 3.0 31.6 - - - -
562A PHE* 3.7 28.0 - + + +
563A GLU* 4.6 1.3 - - - +
582A TYR* 3.3 5.3 - - - +
583A PHE* 2.8 53.7 + - + +
585A GLN* 4.0 22.0 - - + -
630A LEU* 1.3 81.5 - - - +
632A SER* 1.3 61.1 + - - +
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Residues in contact with SER 632 (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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560A LEU* 3.6 7.0 - - - +
561A LYS* 2.8 42.2 + - - +
563A GLU* 6.3 3.4 - - - -
580A LYS* 3.0 37.4 - - - +
581A MET 2.7 21.5 + - - -
582A TYR* 3.5 13.7 - - - -
583A PHE* 4.1 2.9 - - - -
631A TYR* 1.3 75.3 - - - +
633A LEU* 1.3 60.2 + - - +
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Residues in contact with LEU 633 (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* 3.4 50.3 - - + +
559A LYS* 3.6 30.5 - - + +
560A LEU* 3.7 24.2 - - + +
580A LYS* 3.5 5.2 - - - +
581A MET* 3.0 45.0 + - + +
583A PHE* 5.1 0.2 - - + -
632A SER* 1.3 73.6 + - - +
634A SER* 1.3 85.0 + - - +
637A ASN* 3.6 11.4 - - + +
638A PHE* 4.3 8.1 - - + +
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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