Contacts of the strand formed by residues 395 - 404 (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 ILE 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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340A TYR* 4.5 3.6 - - + -
359A LEU* 4.4 9.6 - - + -
360A PHE 3.8 5.4 - - - +
361A GLY* 3.9 0.9 - - - -
392A VAL* 3.6 22.4 - - + -
393A GLY 3.4 4.2 + - - +
394A THR* 1.3 79.3 - - - +
396A GLU* 1.3 59.6 + - - +
397A LYS 3.9 15.0 - - - +
398A VAL* 4.2 8.1 - - + -
422A VAL* 3.4 33.0 - - + -
424A LYS* 3.7 24.5 - - + -
432A PHE* 3.4 36.7 - - + -
448A PRO* 5.5 1.2 - - - +
701A HIS* 4.6 16.2 + - + +
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Residues in contact with GLU 396 (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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360A PHE 2.8 13.1 + - - +
361A GLY 4.0 7.6 - - - +
362A SER* 3.6 28.6 - - - +
394A THR* 3.3 17.4 + - + +
395A ILE* 1.3 74.1 - - - +
397A LYS* 1.3 64.0 + - + +
432A PHE* 3.6 2.8 - - - -
448A PRO* 3.5 25.8 - - - +
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Residues in contact with LYS 397 (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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360A PHE* 2.9 56.3 + - + +
395A ILE* 3.9 1.2 - - - +
396A GLU* 1.3 81.2 - - + +
398A VAL* 1.3 67.4 + - - +
399A LYS* 4.1 21.1 - - - +
432A PHE* 3.7 6.8 - - - -
445A THR* 3.9 21.9 + - + +
446A LEU 3.3 17.3 - - - +
447A THR* 4.9 4.9 - - + -
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Residues in contact with VAL 398 (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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357A VAL* 3.2 31.9 - - + -
358A ALA 3.5 5.4 - - - +
359A LEU* 3.8 22.9 - - + -
360A PHE 4.7 0.2 - - - +
395A ILE* 4.2 2.2 - - + -
397A LYS* 1.3 78.7 - - - +
399A LYS* 1.3 67.3 + - - +
420A ILE* 3.6 19.7 - - + -
422A VAL* 3.9 7.9 - - + -
432A PHE* 3.9 34.5 - - + -
444A LEU 3.7 0.3 - - - +
445A THR* 3.5 2.8 - - - +
446A LEU* 2.9 32.9 + - + +
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Residues in contact with LYS 399 (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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357A VAL* 3.2 6.8 - - - +
358A ALA* 2.8 36.6 + - + +
360A PHE* 3.5 45.5 - - + -
368A GLN* 5.7 0.9 - - - +
397A LYS* 4.1 22.9 - - + +
398A VAL* 1.3 79.4 - - - +
400A PHE* 1.3 61.2 + - - +
401A LEU* 5.4 0.3 - - - +
443A LEU* 4.0 38.2 - - + +
444A LEU 3.2 5.6 - - - +
445A THR* 3.5 27.3 + - + +
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Residues in contact with PHE 400 (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* 4.2 12.3 - - + -
346A LEU* 4.0 13.2 - - + -
355A ALA* 3.7 24.7 - - + -
356A LYS 3.5 11.7 - - - -
357A VAL* 4.7 1.3 - - - +
398A VAL 4.1 1.2 + - - -
399A LYS* 1.3 72.7 - - - +
401A LEU* 1.3 68.0 + - - +
402A TRP* 3.9 27.1 - + + -
415A VAL* 3.8 37.7 - - + -
416A GLY* 4.0 17.0 - - - -
417A ALA* 4.0 12.8 - - + -
420A ILE* 4.2 5.8 - - + -
438A VAL* 4.5 2.0 - - + -
442A VAL 3.7 1.0 - - - +
443A LEU* 3.6 2.9 - - - +
444A LEU* 2.8 42.4 + - + +
446A LEU* 4.0 20.2 - - + -
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Residues in contact with LEU 401 (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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355A ALA* 3.5 0.9 - - - -
356A LYS* 2.6 62.0 + - + +
368A GLN* 3.0 35.9 - - + +
399A LYS 5.4 0.7 - - - +
400A PHE* 1.3 80.9 - - - +
402A TRP* 1.3 61.7 + - - +
403A ASN* 4.8 2.9 - - - +
441A ASP* 3.3 23.6 - - - +
442A VAL 3.2 46.4 - - - +
443A LEU* 3.8 13.9 - - + +
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Residues in contact with TRP 402 (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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351A ALA* 3.9 22.2 - - + -
352A THR 4.0 3.1 - - - -
354A GLN 3.0 11.9 - - - +
355A ALA* 4.2 3.8 - - - -
356A LYS* 5.3 0.2 - - - -
376A LEU* 3.9 19.3 - - + -
400A PHE* 3.9 22.0 - + + -
401A LEU* 1.3 77.1 - - - +
403A ASN* 1.3 62.3 + - - +
404A ASN* 3.3 44.6 - - + -
413A PRO* 3.7 25.4 - - + -
415A VAL* 3.4 36.1 - - + +
438A VAL* 3.1 23.9 + - + -
439A ARG 3.4 10.1 - - - -
440A GLU* 3.4 24.6 - - + -
441A ASP* 2.7 29.1 + - - +
442A VAL 4.8 0.2 + - - -
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Residues in contact with ASN 403 (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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353A GLY* 3.2 2.6 - - - -
354A GLN* 2.8 37.6 + - + +
356A LYS* 3.0 33.3 - - - +
401A LEU* 4.8 4.8 - - - +
402A TRP* 1.3 83.2 - - - +
404A ASN* 1.3 66.4 + - - +
406A ASN* 4.0 2.4 + - - +
440A GLU* 4.6 1.6 - - - -
441A ASP* 2.8 30.4 + - - +
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Residues in contact with ASN 404 (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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352A THR 3.5 8.3 - - - +
402A TRP* 3.3 25.2 - - + -
403A ASN* 1.3 77.2 - - - +
406A ASN* 1.3 71.6 + - - +
409A ASN* 5.0 12.1 - - - +
440A GLU* 3.4 35.1 + - - +
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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