Contacts of the strand formed by residues 324 - 333 (chain C) in PDB entry 3RBH
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 TRP 324 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320C ILE* 2.9 42.0 + - + +
321C ASP* 2.8 32.8 + - - +
323C GLN* 1.3 81.3 + - + +
325C LYS* 1.3 68.9 + - - +
385C SER 3.6 15.0 - - - -
386C TRP* 3.5 38.4 - + + +
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Residues in contact with LYS 325 (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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265C ASN 4.9 1.0 + - - -
266C TYR* 2.9 26.5 + - - +
268C SER 5.1 2.0 - - - +
317C ARG* 4.2 5.8 - - - +
318C TRP 3.3 9.2 - - - +
319C ASN* 2.9 37.0 + - + +
320C ILE* 4.2 4.7 - - - +
321C ASP 4.9 5.2 - - - -
322C GLU 4.9 6.4 + - - -
323C GLN 4.5 4.0 - - - +
324C TRP* 1.3 84.0 - - - +
326C ALA* 1.3 62.0 + - - +
357C THR 4.1 6.7 - - - +
358C GLY* 2.8 33.1 + - - +
383C PHE* 5.3 1.1 - - + -
384C GLY* 3.3 4.0 - - - -
385C SER* 3.0 46.8 + - - +
387C GLN* 3.5 11.6 + - - +
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Residues in contact with ALA 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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317C ARG* 3.5 1.4 - - - +
318C TRP* 2.7 40.5 + - + +
320C ILE* 4.2 15.4 - - + +
325C LYS* 1.3 76.9 - - - +
327C GLY* 1.3 58.9 + - - +
383C PHE* 3.3 18.2 - - - +
384C GLY* 4.3 2.2 - - - -
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Residues in contact with GLY 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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316C LEU* 3.0 14.8 - - - -
326C ALA* 1.3 77.6 - - - +
328C VAL* 1.3 68.8 + - - +
382C LEU* 3.7 1.6 - - - +
383C PHE* 3.0 46.6 + - - +
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Residues in contact with VAL 328 (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 TRP* 4.4 2.4 - - - -
315C GLY* 3.3 2.3 - - - -
316C LEU* 2.9 54.6 + - + +
327C GLY* 1.3 80.7 - - - +
329C GLY* 1.3 61.1 + - - +
381C THR 3.3 9.2 - - - +
382C LEU* 3.8 19.1 - - + -
383C PHE* 3.7 5.1 - - - -
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Residues in contact with GLY 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 TRP* 4.7 2.9 - - - -
314C LEU 3.2 11.4 - - - -
315C GLY* 4.1 2.0 - - - -
328C VAL* 1.3 79.1 - - - +
330C TYR* 1.3 62.3 + - - +
365C ARG* 3.9 12.8 - - - -
380C ALA* 3.6 3.8 - - - +
381C THR* 2.9 36.9 + - - +
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Residues in contact with TYR 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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312C VAL* 4.4 10.8 - - + -
313C ASP* 3.4 1.9 - - - +
314C LEU* 2.7 60.2 + - + +
329C GLY* 1.3 75.0 - - - +
331C ALA* 1.3 62.6 + - - +
332C ARG* 3.4 32.9 - - + +
365C ARG* 3.7 3.3 - - - +
378C GLN* 2.8 46.2 + - + +
379C ALA 3.4 16.6 - - - -
380C ALA* 4.8 6.1 - - + -
402C TRP* 5.5 2.0 - + - -
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Residues in contact with ALA 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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312C VAL 3.2 13.5 - - - +
313C ASP* 3.9 11.7 - - + +
330C TYR* 1.3 85.9 - - - +
332C ARG* 1.3 62.6 + - - +
365C ARG* 4.1 2.0 - - - +
366C PHE* 3.6 37.9 - - + -
374C LEU* 4.2 4.9 - - + +
377C LEU 4.0 0.2 - - - +
378C GLN* 3.5 1.2 - - - -
379C ALA* 3.0 30.7 + - + +
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Residues in contact with ARG 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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310C PHE* 4.1 9.1 + - - +
311C GLY* 3.2 2.6 - - - -
312C VAL* 2.8 43.7 + - + +
330C TYR* 3.4 29.2 + - + +
331C ALA* 1.3 75.6 - - - +
333C GLY* 1.3 60.2 + - - +
334C SER* 3.7 28.1 - - - +
374C LEU* 3.7 6.3 - - - +
377C LEU 3.3 10.1 - - - +
378C GLN* 4.5 9.8 - - + +
404C VAL* 3.1 36.5 - - + +
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Residues in contact with GLY 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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310C PHE 3.6 6.3 - - - -
332C ARG* 1.3 75.6 - - - +
334C SER* 1.3 70.9 + - - +
344C PHE* 3.8 11.2 - - - -
374C LEU* 3.6 20.9 - - - +
376C ASN* 2.9 15.8 + - - -
377C LEU 2.9 17.9 + - - +
404C VAL* 3.7 3.1 - - - +
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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