Contacts of the strand formed by residues 415 - 424 (chain A) in PDB entry 1RP1
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 VAL 415 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A LEU* 4.3 8.3 - - + -
347A SER 3.9 8.3 - - - +
349A LYS 3.8 15.0 - - - +
351A ALA* 3.8 16.4 - - + -
376A LEU* 4.2 20.6 - - + +
400A PHE* 3.8 17.5 - - + -
402A TRP* 3.4 37.6 - - + +
414A LYS* 1.3 77.4 - - - +
416A GLY* 1.3 70.1 + - - +
437A THR* 3.9 1.1 - - - -
438A VAL* 2.8 36.6 + - - +
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Residues in contact with GLY 416 (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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346A LEU* 3.6 16.1 - - - +
347A SER* 3.0 36.8 + - - +
400A PHE* 4.0 9.6 - - - -
415A VAL* 1.3 77.0 - - - +
417A ALA* 1.3 59.6 + - - -
436A SER 3.8 13.2 - - - -
437A THR* 3.9 3.0 - - - -
444A LEU* 4.1 4.0 - - - -
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Residues in contact with ALA 417 (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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344A ILE* 3.7 27.4 - - + -
345A THR 3.4 6.5 - - - +
347A SER* 3.3 2.4 + - - -
400A PHE* 4.0 11.9 - - + -
416A GLY* 1.3 73.5 - - - -
418A ALA* 1.3 64.6 + - - +
419A LYS 4.5 0.2 - - - +
420A ILE* 3.9 22.9 - - + -
434A SER* 3.7 15.4 - - - +
436A SER 4.4 0.4 + - - +
444A LEU* 3.7 5.9 - - - +
446A LEU* 3.6 14.0 - - + +
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Residues in contact with ALA 418 (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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345A THR* 3.0 16.8 + - + +
346A LEU 4.8 2.9 - - - +
347A SER* 3.7 19.9 + - - -
417A ALA* 1.3 74.3 - - - +
419A LYS* 1.3 63.2 + - + +
433A CYS* 3.3 9.2 - - - +
434A SER 3.2 33.1 + - - +
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Residues in contact with LYS 419 (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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343A SER 3.7 1.6 - - - +
345A THR* 3.0 41.6 + - + +
417A ALA 3.2 1.0 - - - -
418A ALA* 1.3 84.5 - - + +
420A ILE* 1.3 73.3 + - - +
421A THR* 4.3 11.0 - - + +
431A SER* 3.5 31.1 + - - -
432A PHE 3.2 12.6 - - - +
433A CYS* 4.0 14.8 - - - -
446A LEU* 4.0 0.7 - - - -
449A CYS* 4.3 2.3 - - - -
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Residues in contact with ILE 420 (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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342A VAL* 4.4 9.0 - - + -
343A SER 3.2 8.5 - - - +
344A ILE* 4.1 15.5 - - + -
357A VAL* 3.7 18.2 - - + -
398A VAL* 3.6 33.7 - - + -
400A PHE* 4.2 7.2 - - + -
417A ALA* 3.9 15.3 - - + -
419A LYS* 1.3 78.8 - - - +
421A THR* 1.3 70.2 + - - +
422A VAL* 4.2 9.6 - - + -
431A SER* 3.6 0.7 - - - -
432A PHE* 2.8 38.0 + - + +
446A LEU* 3.7 26.2 - - + -
701A HIS 3.7 1.2 - - - +
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Residues in contact with THR 421 (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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342A VAL* 3.2 7.4 - - - +
343A SER* 3.0 50.8 + - - +
419A LYS* 4.3 14.1 - - + +
420A ILE* 1.3 75.0 - - - +
422A VAL* 1.3 62.0 + - - +
430A VAL* 3.7 19.6 - - + +
431A SER* 3.6 22.9 - - - +
701A HIS 3.1 3.6 - - - -
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Residues in contact with VAL 422 (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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340A TYR* 4.5 10.1 - - + -
341A GLY 3.4 8.5 - - - +
342A VAL* 4.3 2.9 - - + -
359A LEU* 4.0 19.3 - - + -
395A ILE* 3.4 30.1 - - + -
398A VAL* 3.9 18.8 - - + -
420A ILE* 4.2 7.6 - - + -
421A THR* 1.3 80.3 - - - +
423A GLN* 1.3 64.7 + - - +
430A VAL* 3.5 6.0 - - - -
432A PHE* 3.9 25.6 - - + -
701A HIS* 2.7 38.8 + - + +
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Residues in contact with GLN 423 (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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297A PHE* 3.3 24.4 - - + -
298A PRO* 4.0 23.2 - - + +
340A TYR* 3.4 3.1 - - - +
341A GLY 2.9 40.7 + - - +
422A VAL* 1.3 76.3 - - - +
424A LYS* 1.3 69.8 + - - +
427A GLU 3.1 19.4 - - - +
428A LYS 4.3 6.7 + - - -
429A THR 3.0 21.6 + - - +
430A VAL* 3.6 23.8 - - + +
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Residues in contact with LYS 424 (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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297A PHE* 4.2 0.4 - - - -
339A ARG 4.3 0.2 - - - -
340A TYR* 3.6 30.5 - - + -
391A ASP* 2.5 36.1 + - - -
392A VAL 4.6 1.0 - - - +
393A GLY* 2.8 25.5 + - - +
395A ILE* 3.7 23.8 - - + -
422A VAL 4.4 0.2 + - - -
423A GLN* 1.3 89.5 + - - +
425A GLY* 1.3 66.3 + - - +
426A GLU* 3.2 4.0 + - + +
427A GLU* 3.2 47.0 + - + +
429A THR 4.9 2.0 + - - -
701A HIS* 4.7 5.6 - - + -
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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