Contacts of the strand formed by residues 321 - 329 (chain C) in PDB entry 1RJF
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 TYR 321 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231C TYR* 3.2 37.0 - + - +
232C ASP 3.6 4.9 - - - -
233C PRO* 3.7 26.0 - - + -
243C PHE* 4.2 8.6 - + - -
247C MET* 3.8 16.1 - - + +
285C ASP* 3.2 12.6 - - - +
286C MET* 3.2 14.5 + - + -
317C MET* 3.2 41.9 - - + -
318C GLN* 3.2 22.4 + - - +
319C THR 3.2 0.8 - - - -
320C HIS* 1.3 84.3 - - - +
322C ILE* 1.3 71.4 + - - +
335C BME 3.9 23.8 - - + +
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Residues in contact with ILE 322 (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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230C SER 3.8 10.1 - - - +
231C TYR* 3.2 29.8 - - - -
232C ASP 3.1 18.3 + - - +
234C ILE* 4.1 30.1 - - + -
268C LYS* 4.0 25.4 - - + -
271C TYR* 3.4 42.6 - - + -
283C VAL* 4.6 7.2 - - + -
284C ASN 3.9 6.1 - - - +
285C ASP* 4.1 7.6 - - + -
286C MET* 3.6 5.8 - - - -
321C TYR* 1.3 81.2 - - - +
323C LEU* 1.3 62.4 + - - +
324C MET* 4.1 7.9 - - + -
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Residues in contact with LEU 323 (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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81C ARG 5.4 0.4 - - - +
84C GLY* 3.3 34.3 - - - +
85C ILE* 3.7 30.7 - - + +
88C ALA* 5.3 0.9 - - + -
229C ILE* 3.7 17.5 - - + -
230C SER 3.9 2.0 - - - +
231C TYR* 4.6 12.3 - - + -
282C ILE* 5.8 0.5 - - - +
283C VAL* 3.8 3.1 - - - -
284C ASN* 3.2 26.0 + - - +
286C MET* 3.9 6.5 - - + -
289C ILE* 3.7 27.4 - - + +
293C GLN* 5.1 4.5 - - - +
322C ILE* 1.3 78.7 - - - +
324C MET* 1.3 60.0 + - - +
325C LYS* 4.1 18.5 + - + +
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Residues in contact with MET 324 (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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228C TRP* 2.9 27.4 - - + +
229C ILE* 3.4 2.6 - - - -
230C SER* 3.1 34.1 + - - +
271C TYR* 4.2 5.6 - - + -
272C ALA* 4.3 24.5 - - + -
275C TRP* 3.3 48.0 - - + +
281C VAL* 4.4 5.8 - - + -
282C ILE 3.8 10.3 - - - +
283C VAL* 4.2 3.8 - - + -
322C ILE* 4.1 12.6 - - + -
323C LEU* 1.3 73.9 - - - +
325C LYS* 1.3 64.9 + - - +
326C ALA* 3.6 23.8 - - + -
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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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88C ALA* 3.7 31.7 - - + +
91C GLU* 4.1 19.8 + - - -
227C LEU* 4.0 14.4 - - + -
228C TRP 3.5 3.4 - - - -
229C ILE* 5.0 2.7 - - + -
280C ASN 4.0 0.4 - - - +
281C VAL* 3.6 2.3 - - - -
282C ILE* 3.1 68.9 + - + +
284C ASN* 5.9 1.1 - - - +
293C GLN* 5.3 12.3 - - - +
323C LEU* 4.1 16.1 + - + +
324C MET* 1.3 76.9 - - - +
326C ALA* 1.3 62.2 + - - +
327C GLN* 4.2 3.8 - - + +
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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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227C LEU* 3.9 2.4 - - - +
228C TRP* 3.1 24.4 + - + +
275C TRP* 4.0 25.4 - - + -
278C ALA* 4.4 8.5 - - + -
280C ASN 3.4 8.7 - - - +
281C VAL* 4.4 2.7 - - + -
324C MET* 3.6 20.0 - - + -
325C LYS* 1.3 75.3 - - - +
327C GLN* 1.3 62.6 + - - +
328C TRP* 3.1 19.9 - - + -
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Residues in contact with GLN 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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91C GLU* 5.7 2.8 + - - -
92C PHE* 3.5 30.0 - - - -
225C HIS* 4.9 5.2 + - - +
226C GLY 3.5 7.0 - - - +
227C LEU* 3.8 24.4 - - + +
278C ALA* 3.7 1.4 - - - +
279C PRO* 3.6 3.5 - - - +
280C ASN* 3.1 55.4 + - + +
282C ILE* 5.9 3.0 - - - +
325C LYS* 5.5 3.5 - - + +
326C ALA* 1.3 73.6 - - - +
328C TRP* 1.3 61.4 + - - +
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Residues in contact with TRP 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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196C THR 4.6 3.4 - - - -
198C VAL* 4.9 6.5 - - + -
219C ILE 4.6 3.6 - - - -
220C MET* 3.2 68.3 + - + -
223C PHE* 3.4 18.8 + + + -
224C SER 3.4 17.0 + - - +
225C HIS* 3.7 6.8 - - - -
226C GLY* 3.5 30.8 + - - +
227C LEU 3.7 12.8 - - - -
228C TRP* 3.7 28.5 - + + -
278C ALA* 3.8 16.2 - - + -
279C PRO* 4.0 10.1 - - + -
326C ALA 3.1 28.3 - - - -
327C GLN* 1.3 76.2 - - - +
329C HIS* 1.3 62.8 + - - +
330C HIS* 4.4 9.9 - - + -
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Residues in contact with HIS 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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224C SER* 3.6 8.9 - - - -
225C HIS* 3.2 46.6 + + + +
279C PRO* 4.7 9.5 - - - +
328C TRP* 1.3 73.1 - - - +
330C HIS* 1.3 64.8 + - - +
331C HIS* 3.5 40.7 + + + -
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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