Contacts of the strand formed by residues 495 - 502 (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 ARG 495 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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488A SER* 2.7 41.1 + - - +
489A PHE 4.8 1.1 - - - -
490A SER* 4.2 8.7 - - - +
493A GLY 3.1 12.1 + - - +
494A LYS* 1.3 73.6 - - - +
496A ARG* 1.3 62.5 + - - +
497A GLY* 3.4 11.7 - - - +
498A GLU* 3.8 7.7 + - - -
512A HIS 3.9 4.5 - - - +
514A ALA* 3.7 7.3 - - - +
520A VAL* 3.8 18.2 - - + -
566A TRP* 3.2 40.6 + - + -
569A GLU 5.8 0.2 - - - +
637A ALA* 6.0 0.6 - - - +
644A VAL* 3.5 37.9 + - - +
645A LEU 3.3 22.6 + - - -
646A GLY* 4.0 8.5 - - - -
647A ALA* 5.4 0.4 - - - +
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Residues in contact with ARG 496 (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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469A ARG 5.7 2.1 + - - -
495A ARG* 1.3 73.2 - - - +
497A GLY* 1.3 63.5 + - - +
512A HIS* 2.9 27.1 + - + +
513A ASN 3.7 11.7 - - - -
514A ALA* 3.9 10.7 - - + +
515A PHE* 4.0 30.0 - - - +
565A HIS* 3.3 5.5 - - - +
566A TRP* 3.0 51.1 + - + +
567A GLU* 2.8 36.3 + - - +
568A VAL 3.7 11.2 + - - +
569A GLU* 3.9 21.7 - - - +
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Residues in contact with GLY 497 (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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488A SER* 3.8 14.0 + - - -
495A ARG* 3.4 10.3 - - - +
496A ARG* 1.3 79.4 - - - +
498A GLU* 1.3 66.5 + - - +
511A ALA* 3.5 2.6 - - - +
512A HIS* 2.9 26.9 + - - +
564A SER 3.4 10.8 - - - -
565A HIS* 4.0 0.7 - - - -
566A TRP* 3.8 13.6 - - - -
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Residues in contact with GLU 498 (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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486A CYS* 3.5 40.3 - - - +
487A SER* 3.8 6.6 - - - +
488A SER* 2.8 39.4 + - - -
495A ARG* 3.8 6.2 + - - -
497A GLY* 1.3 75.8 - - - +
499A ARG* 1.3 61.4 + - - +
510A ARG 3.3 13.9 - - - +
511A ALA* 4.1 2.5 - - - -
512A HIS* 4.6 0.9 - - - -
562A CYS 4.6 0.5 - - - +
563A SER* 3.2 10.3 - - - -
564A SER 2.9 62.5 + - - +
565A HIS* 3.4 7.9 + - - +
597A HIS* 3.7 0.5 - - - -
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Residues in contact with ARG 499 (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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486A CYS* 3.8 4.0 - - - -
498A GLU* 1.3 74.0 - - - +
500A MET* 1.3 64.8 + - - +
501A GLU* 2.8 35.2 + - + -
510A ARG* 2.9 50.6 + - + +
512A HIS* 3.5 31.4 + - + +
563A SER* 4.3 2.0 - - - -
565A HIS* 4.1 22.3 + - - +
597A HIS* 3.4 30.1 - - + +
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Residues in contact with MET 500 (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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483A LEU* 4.0 18.2 - - + +
484A LEU 4.8 0.2 - - - -
485A SER* 4.2 12.3 - - - -
486A CYS* 3.4 26.7 - - + -
499A ARG* 1.3 76.7 - - - +
501A GLU* 1.3 60.8 + - - +
507A LEU* 5.1 0.4 - - + -
508A VAL 3.3 7.4 - - - +
536A VAL* 3.8 34.1 - - + +
538A THR* 5.0 0.5 + - - -
561A GLY 4.2 5.6 - - - +
563A SER* 3.4 19.5 - - - +
597A HIS* 3.6 34.2 + - + +
598A ALA 4.0 1.3 - - - +
599A SER* 3.6 37.9 - - - +
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Residues in contact with GLU 501 (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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499A ARG* 2.8 42.0 + - - +
500A MET* 1.3 74.0 - - - +
502A ALA* 1.3 67.7 + - - +
503A GLN* 3.7 7.6 - - - +
507A LEU* 3.5 9.3 - - - +
508A VAL* 2.8 39.1 + - + +
510A ARG* 3.4 39.1 + - + +
536A VAL* 6.1 0.2 - - - -
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Residues in contact with ALA 502 (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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501A GLU* 1.3 79.7 - - - +
503A GLN* 1.3 62.5 - - - +
504A GLY 4.3 0.2 - - - -
505A GLY* 5.0 5.4 - - - +
506A LYS 3.5 14.6 - - - +
507A LEU* 3.5 16.8 - - + +
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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