Contacts of the strand formed by residues 325 - 334 (chain C) 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 ALA 325 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74C ASN* 3.6 33.2 - - + +
320C VAL 3.3 0.5 - - - +
321C THR* 3.9 3.4 - - - -
322C ILE 2.8 38.4 + - - +
323C ASP 3.1 0.2 - - - -
324C TYR* 1.3 81.5 - - - +
326C GLU* 1.3 63.5 + - - +
327C ILE* 3.3 16.2 + - + +
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Residues in contact with GLU 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C LYS* 3.4 48.7 - - + +
320C VAL 3.5 4.0 - - - +
321C THR* 4.1 20.3 + - + +
324C TYR 4.3 0.2 + - - -
325C ALA* 1.3 70.3 - - - +
327C ILE* 1.3 66.1 + - - +
328C SER* 4.0 3.7 + - - +
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Residues in contact with ILE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C THR* 4.4 13.7 - - + -
275C VAL* 3.9 26.2 - - + -
318C VAL 3.3 0.7 - - - +
319C LYS* 4.6 0.9 - - - -
320C VAL 2.7 37.5 + - - +
322C ILE* 4.1 17.3 - - + -
325C ALA* 3.7 22.9 - - + +
326C GLU* 1.3 80.4 - - - +
328C SER* 1.3 67.6 + - - +
329C PHE* 3.3 36.8 - - + -
343C PRO* 4.9 4.9 - - + -
344C LYS 5.4 0.4 - - - +
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Residues in contact with SER 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C VAL* 4.0 16.2 - - - +
318C VAL 3.4 5.6 - - - -
319C LYS* 3.4 23.8 - - - +
326C GLU* 4.0 4.0 + - - +
327C ILE* 1.3 73.3 - - - +
329C PHE* 1.3 56.8 + - - +
343C PRO* 3.3 2.9 - - - +
344C LYS* 2.7 43.3 + - - -
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Residues in contact with PHE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275C VAL* 5.6 2.0 - - + -
297C LEU* 5.8 3.8 - - + -
302C PHE* 6.0 1.6 - + - -
317C VAL* 3.2 8.8 - - - +
318C VAL* 2.8 37.0 + - + +
320C VAL* 4.1 20.2 - - + -
322C ILE* 4.2 13.7 - - + -
327C ILE* 3.3 40.8 - - + -
328C SER* 1.3 74.5 - - - +
330C MET* 1.3 60.2 + - - +
341C PHE* 3.6 46.7 - + + -
342C TYR 3.2 22.0 - - - +
343C PRO* 3.5 21.3 - - + -
344C LYS 3.9 4.9 - - - -
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Residues in contact with MET 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315C SER* 4.2 14.1 - - - +
316C LYS 3.6 17.9 - - - +
317C VAL* 3.7 22.2 - - - -
329C PHE* 1.3 71.2 - - - +
331C LEU* 1.3 59.3 + - - +
332C TRP* 3.7 33.4 - - + +
340C THR 3.8 1.0 - - - +
341C PHE* 3.3 26.5 + - - -
342C TYR* 2.7 46.7 + - + +
344C LYS 3.9 14.5 + - - +
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Residues in contact with LEU 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C ILE* 4.9 3.8 - - + -
309C GLN* 4.3 19.3 - - + -
310C ASP 4.2 9.9 - - - +
311C LEU* 5.2 0.4 - - + -
313C VAL 4.9 2.0 - - - +
315C SER* 3.0 4.2 - - - -
316C LYS* 2.8 60.3 + - + +
318C VAL* 3.7 18.2 - - + -
329C PHE 3.9 0.2 + - - -
330C MET* 1.3 72.5 - - - +
332C TRP* 1.3 69.5 + - - +
333C CYS* 3.5 28.9 - - - -
338C VAL* 4.1 18.6 - - + -
340C THR 3.9 1.6 - - - +
341C PHE* 3.8 20.0 - - + -
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Residues in contact with TRP 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C ILE* 3.3 18.8 - - + -
315C SER* 3.7 24.9 - - - -
330C MET* 3.7 26.6 - - + +
331C LEU* 1.3 79.7 - - - +
333C CYS* 1.3 66.4 + - - +
338C VAL 3.8 0.3 - - - -
339C GLU* 2.9 32.1 + - + +
340C THR* 3.1 40.8 + - + +
342C TYR* 3.2 29.8 + + - -
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Residues in contact with CYS 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C LEU* 3.6 38.4 - - - +
312C SER 5.0 2.1 - - - +
313C VAL 3.4 15.2 - - - +
314C ILE* 2.7 37.9 + - - +
331C LEU* 3.5 31.4 - - - -
332C TRP* 1.3 81.4 - - - +
334C LYS* 1.3 61.6 + - - +
336C GLY 5.5 0.2 - - - +
337C HIS 3.5 10.8 - - - +
338C VAL* 4.4 4.0 - - - -
339C GLU* 3.8 4.0 - - - +
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Residues in contact with LYS 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314C ILE* 5.8 1.3 - - - -
333C CYS* 1.3 75.0 - - - +
335C ASP* 1.3 87.5 + - - +
336C GLY 3.3 2.2 - - - -
337C HIS* 2.9 23.7 + - - +
339C GLU* 3.4 28.5 - - - +
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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