Contacts of the strand formed by residues 507 - 513 (chain A) in PDB entry 2P4E
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 507 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477A CYS* 5.3 5.0 + - - -
482A GLU* 6.1 0.7 - - - +
483A LEU* 3.7 36.6 - - + +
501A GLU* 3.5 8.3 - - - +
502A ALA* 3.5 31.2 - - + +
506A LYS* 1.3 84.7 + - - +
508A VAL* 1.3 61.5 + - - +
534A CYS* 4.2 24.9 - - + +
535A SER* 4.8 2.9 - - - -
536A VAL* 3.8 32.8 - - + +
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Residues in contact with VAL 508 (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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474A ILE* 3.9 18.4 - - + -
475A ALA 4.0 4.0 - - - +
476A ARG* 3.8 32.1 - - + +
477A CYS 5.8 0.2 - - - +
483A LEU* 3.5 8.1 - - - +
500A MET* 3.3 6.2 - - - -
501A GLU* 2.8 52.0 + - + +
503A GLN* 3.9 36.6 - - + +
506A LYS* 4.0 5.4 - - + +
507A LEU* 1.3 77.3 - - - +
509A CYS* 1.3 62.9 + - - +
510A ARG* 3.9 3.9 + - + +
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Residues in contact with CYS 509 (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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474A ILE* 3.3 4.9 - - - -
475A ALA* 2.9 42.0 + - + +
483A LEU* 3.8 4.9 - - + +
486A CYS* 2.0 57.4 - - + -
487A SER 3.8 8.5 - - - -
508A VAL* 1.3 74.5 - - - +
510A ARG* 1.3 58.2 + - - +
522A ALA* 3.6 7.2 - - - +
523A ILE 3.6 20.6 - - - -
524A ALA* 4.0 12.8 - - + -
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Residues in contact with ARG 510 (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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472A THR* 2.8 49.3 + - + +
473A ALA 3.3 9.2 - - - +
474A ILE* 3.3 25.7 - - + +
498A GLU* 3.3 5.1 - - - +
499A ARG* 2.9 55.0 + - + +
501A GLU* 3.4 34.3 + - + -
503A GLN* 2.8 29.3 + - - -
508A VAL* 3.9 3.4 + - + +
509A CYS* 1.3 74.0 - - - +
511A ALA* 1.3 60.5 + - - +
512A HIS* 4.2 8.1 - - + -
522A ALA* 4.5 0.2 - - - -
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Residues in contact with ALA 511 (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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472A THR* 3.2 10.6 - - - -
473A ALA* 2.9 29.0 + - + +
488A SER* 3.8 16.4 - - - -
497A GLY 3.5 4.0 - - - -
498A GLU* 4.1 1.3 - - + -
510A ARG* 1.3 74.1 - - - +
512A HIS* 1.3 64.3 + - - +
520A VAL* 3.9 11.4 - - + +
521A TYR 3.8 6.5 - - - +
522A ALA* 3.7 32.9 - - + +
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Residues in contact with HIS 512 (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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470A MET 6.2 0.4 - - - -
471A ALA 3.9 2.4 + - - -
472A THR* 3.7 26.0 - - + +
495A ARG* 3.9 0.2 - - - -
496A ARG* 2.9 47.5 + - + -
497A GLY 2.9 14.7 + - - +
499A ARG* 3.5 40.0 + - + +
510A ARG* 4.2 11.7 - - - -
511A ALA* 1.3 73.3 - - - +
513A ASN* 1.3 62.1 + - - +
514A ALA 3.6 0.2 + - - -
520A VAL* 3.6 9.9 - - - +
565A HIS* 3.9 33.4 - + + -
566A TRP 5.8 0.2 - - - -
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Residues in contact with ASN 513 (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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465A SER* 4.2 4.3 - - - +
466A GLY 3.5 2.2 - - - +
467A PRO 3.3 8.8 - - - +
468A THR 2.9 20.2 - - - +
469A ARG 4.2 7.2 - - - +
470A MET* 5.4 0.5 - - - -
471A ALA* 3.1 31.5 + - + +
494A LYS 3.8 4.9 + - - -
496A ARG* 3.7 12.9 - - - -
512A HIS* 1.3 76.6 - - - +
514A ALA* 1.3 77.5 + - - +
515A PHE 3.9 0.2 + - - -
517A GLY* 3.3 24.2 - - - +
519A GLY* 3.2 32.6 - - - +
520A VAL* 3.5 9.6 - - - +
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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