Contacts of the strand formed by residues 315 - 322 (chain D) in PDB entry 2RHB
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 SER 315 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313D VAL* 3.3 12.9 - - - +
314D ILE* 1.3 88.9 - - - +
316D LYS* 1.3 61.5 + - - +
330D MET* 5.3 5.8 - - - -
331D LEU 3.3 9.4 - - - -
332D TRP* 3.7 37.7 - - - -
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Residues in contact with LYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D VAL* 5.1 11.6 + - + -
315D SER* 1.3 75.5 - - - +
317D VAL* 1.3 65.2 + - - +
318D VAL* 3.9 8.9 + - + -
329D PHE 3.7 1.0 - - - +
330D MET* 3.8 4.7 - - - +
331D LEU* 3.1 47.4 + - + +
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Residues in contact with VAL 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316D LYS* 1.3 73.5 - - - +
318D VAL* 1.3 63.7 + - - +
319D LYS* 4.3 14.9 + - - +
328D SER* 4.4 13.2 - - - +
329D PHE 3.5 2.9 - - - +
330D MET* 3.6 27.1 - - - -
344D LYS* 3.8 28.3 - - + -
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Residues in contact with VAL 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D GLN* 2.9 40.8 - - - +
316D LYS* 4.4 15.3 - - + +
317D VAL* 1.3 78.3 - - - +
319D LYS* 1.3 77.5 + - - +
320D VAL* 4.1 9.6 - - + -
327D ILE 3.5 1.7 - - - +
328D SER* 3.3 5.7 - - - -
329D PHE* 2.9 44.3 + - + +
331D LEU* 4.4 17.7 - - + -
341D PHE* 4.7 2.9 - - + -
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Residues in contact with LYS 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317D VAL* 4.4 17.0 - - - +
318D VAL* 1.3 80.0 - - - +
320D VAL* 1.3 66.0 + - - +
321D THR* 4.3 0.7 - - - +
326D GLU* 3.2 45.1 + - + +
327D ILE 3.7 2.0 - - - -
328D SER* 3.4 24.7 - - - +
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Residues in contact with VAL 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D TYR* 4.2 9.4 - - + -
305D ILE* 3.8 43.3 - - + -
309D GLN* 5.3 0.2 - - - +
318D VAL* 4.1 12.3 - - + -
319D LYS* 1.3 79.0 - - - +
321D THR* 1.3 58.8 + - - +
322D ILE* 3.3 25.0 + - + -
326D GLU* 4.5 0.9 - - - -
327D ILE* 2.7 40.6 + - - +
329D PHE* 3.7 29.4 - - + -
341D PHE* 4.8 1.1 - - + -
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Residues in contact with THR 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D PRO* 3.8 28.3 - - + +
191D GLU 3.4 17.8 + - - +
192D THR* 3.3 17.1 - - + +
193D TYR* 3.0 27.9 + - - -
319D LYS* 4.3 1.1 - - - +
320D VAL* 1.3 69.6 - - - +
322D ILE* 1.3 62.4 + - - +
324D TYR 4.0 13.0 - - - -
325D ALA 3.5 8.3 - - - +
326D GLU* 4.3 10.0 + - + +
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Residues in contact with ILE 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D ASN* 3.9 0.3 + - - -
193D TYR* 3.4 16.6 - - + +
195D THR* 4.0 14.4 - - - +
274D THR* 3.8 21.5 - - + +
295D ILE* 3.8 23.1 - - + -
297D LEU* 4.0 26.2 - - + -
320D VAL* 3.3 24.2 + - + -
321D THR* 1.3 76.7 - - - +
323D ASP* 1.3 67.2 + - - +
324D TYR 3.1 1.8 - - - -
325D ALA* 2.9 30.1 + - - +
327D ILE* 3.8 17.4 - - + +
329D PHE* 4.0 13.5 - - + -
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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