Contacts of the strand formed by residues 324 - 330 (chain C) in PDB entry 1FVU
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 ASN 324 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220C LYS* 3.7 8.8 - - - -
221C MET 3.1 25.4 + - - +
264C ASP* 6.1 0.2 - - - +
266C TYR* 3.9 27.9 + - - +
268C TRP* 3.5 35.6 - - + +
318C LEU* 3.8 11.3 - - - +
322C GLN* 3.1 27.4 + - - +
323C LYS* 1.3 77.1 - - - +
325C PRO* 1.3 81.9 - - + +
326C PHE* 3.6 5.2 - - - -
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Residues in contact with PRO 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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216C PHE* 3.7 12.3 - - + -
217C PHE 3.2 13.0 - - - +
218C GLN* 3.5 14.1 - - - +
219C GLN 3.2 12.3 - - - +
220C LYS* 3.9 12.8 - - + -
260C ILE* 3.8 20.4 - - + -
264C ASP* 4.1 14.4 - - + +
266C TYR 3.1 22.9 - - - +
267C ALA* 3.3 4.5 - - - -
268C TRP* 3.0 18.9 + - - -
324C ASN* 1.3 92.5 - - + +
326C PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 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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216C PHE* 3.5 6.3 - - - -
217C PHE* 2.7 52.7 + - + +
219C GLN* 3.3 20.4 - - + -
221C MET* 4.0 21.5 - - + -
226C ALA* 3.8 15.9 - - + -
229C PHE* 3.5 39.9 - + + -
230C CYS* 3.9 17.0 - - - -
239C LEU* 3.7 17.3 - - + -
267C ALA* 4.4 3.1 - - - -
268C TRP* 3.8 17.3 - - + +
324C ASN 3.6 8.1 - - - -
325C PRO* 1.3 80.8 - - - +
327C VAL* 1.3 64.1 + - - +
328C CYS* 3.7 12.8 - - - -
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Residues in contact with VAL 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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214C TYR* 4.8 6.5 - - + -
215C LYS 3.4 13.0 - - - +
216C PHE* 3.9 7.6 - - + +
230C CYS* 4.4 0.9 - - - -
239C LEU* 3.5 8.8 - - - +
240C VAL* 2.8 50.0 + - + +
252C VAL* 4.2 14.1 - - + -
255C LEU* 5.0 5.6 - - + -
256C VAL* 3.4 33.0 - - + -
267C ALA* 4.7 2.0 - - + -
268C TRP 3.5 7.3 + - - +
306C LEU* 4.7 3.6 - - + -
326C PHE* 1.3 82.5 - - - +
328C CYS* 1.3 74.2 + - - +
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Residues in contact with CYS 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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206C TRP* 3.7 22.7 - - + -
214C TYR* 3.4 4.5 - - - +
215C LYS 2.9 28.4 + - - -
217C PHE* 3.6 23.1 - - + -
229C PHE* 4.3 1.8 - - - -
230C CYS* 2.0 53.4 - - + +
233C GLN* 5.0 0.4 - - - -
237C GLY* 5.9 0.2 - - - -
238C HIS 3.4 4.7 - - - -
326C PHE* 3.7 10.8 - - - -
327C VAL* 1.3 80.1 - - - +
329C LYS* 1.3 61.2 + - - +
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Residues in contact with LYS 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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206C TRP* 4.5 1.3 - - - -
212C ASN* 4.0 24.0 - - + +
213C CYS 3.3 7.0 - - - +
214C TYR* 3.4 35.9 - - + -
236C GLY 3.6 2.1 - - - +
237C GLY* 3.3 2.1 - - - -
238C HIS* 2.8 32.7 + - + +
239C LEU 4.8 0.9 - - - +
240C VAL* 3.8 16.8 - - + -
241C SER* 2.9 36.0 + - - +
243C LYS* 4.5 3.6 - - - +
248C GLU* 3.0 19.8 + - - -
328C CYS* 1.3 75.3 - - - +
330C SER* 1.3 66.0 + - - +
681D ASP* 4.4 7.3 + - - +
683D MET* 4.0 9.5 - - - +
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Residues in contact with SER 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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203C PRO* 5.5 2.4 - - - +
206C TRP* 3.8 10.9 - - - -
212C ASN* 3.6 6.9 - - - +
213C CYS* 2.8 47.1 + - - +
234C ALA* 3.9 26.0 - - - +
235C LYS 4.4 0.4 - - - -
236C GLY 3.7 1.6 - - - -
237C GLY* 3.9 7.9 - - - -
329C LYS* 1.3 78.6 - - - +
331C PRO* 1.3 79.6 + - - +
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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