Contacts of the strand formed by residues 317 - 324 (chain C) in PDB entry 3R2W
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 317 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212C HIS* 6.0 2.0 - - - -
269C MET* 4.8 8.5 - - - +
270C GLU 5.0 0.2 - - - +
271C VAL* 4.5 4.7 - - - -
282C GLY* 3.4 14.6 + - - +
284C LEU* 5.2 8.2 - - + +
293C LEU* 4.5 23.9 - - + +
316C PHE* 1.3 96.0 - - + +
318C THR* 1.3 63.3 + - - +
319C ASN* 3.6 31.1 + - - +
321C LEU* 4.6 12.9 - - - +
362C GLY* 4.8 13.7 - - - +
381C PHE* 5.2 1.9 - - - -
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Residues in contact with THR 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243C ASN* 5.1 0.9 + - - +
270C GLU* 2.5 43.9 + - + +
271C VAL* 3.1 12.3 + - - -
272C THR* 4.0 6.0 + - - +
316C PHE* 3.4 1.9 + - - -
317C ASN* 1.3 73.5 + - - +
319C ASN* 1.3 66.1 + - - +
320C ASN* 3.0 39.7 + - + +
376C VAL* 4.9 1.7 - - + +
380C ARG 4.6 0.7 - - - +
381C PHE* 3.6 40.5 - - + -
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Residues in contact with ASN 319 (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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102C LEU* 4.3 13.5 - - - +
212C HIS* 4.0 24.2 + - - -
238C VAL* 3.6 6.8 - - - +
239C SER* 4.0 4.0 - - - -
240C ASN* 3.4 40.8 - - + +
317C ASN* 3.4 24.2 + - - +
318C THR* 1.3 79.8 - - - +
320C ASN* 1.3 62.5 + - - +
321C LEU* 3.4 22.1 - - - +
361C VAL* 5.0 6.4 - - - +
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Residues in contact with ASN 320 (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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237C PHE* 4.6 3.1 - - + -
238C VAL 3.8 3.4 - - - -
239C SER* 3.6 23.0 - - - +
240C ASN* 4.2 4.2 - - - +
243C ASN* 3.0 31.9 + - - +
246C ALA* 3.7 8.0 - - - +
269C MET* 4.0 0.3 - - - +
270C GLU* 3.0 56.4 + - - +
318C THR* 3.0 24.7 + - + +
319C ASN* 1.3 79.9 + - - +
321C LEU* 1.3 62.1 - - - +
380C ARG* 3.5 8.7 + - - +
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Residues in contact with LEU 321 (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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237C PHE* 3.2 13.8 - - - -
238C VAL* 2.9 42.7 + - + +
267C PHE* 3.6 30.7 - - + -
268C VAL 3.3 9.4 - - - +
269C MET* 4.0 19.3 - - + -
317C ASN* 4.6 8.5 - - - +
319C ASN* 3.4 24.9 - - - +
320C ASN* 1.3 76.7 - - - +
322C TRP* 1.3 66.9 + - - +
323C ILE* 4.7 4.7 - - + -
361C VAL* 3.8 28.0 - - + -
362C GLY* 4.5 15.0 - - - +
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Residues in contact with TRP 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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97C LEU* 4.5 9.9 - - + +
235C TYR* 5.0 7.8 - - + -
236C ILE 3.6 2.7 - - - -
237C PHE* 3.1 50.5 - + + +
247C THR 4.8 0.2 - - - -
248C VAL* 4.9 4.7 - - + -
249C ASP 4.4 16.2 - - - -
252C ILE* 3.3 50.0 - - + -
253C LEU* 4.1 12.2 - - + +
256C LEU* 4.0 24.9 - - + +
267C PHE* 3.7 7.1 - - - -
268C VAL* 3.1 47.8 + - + +
270C GLU* 3.2 35.0 - - + -
321C LEU* 1.3 77.8 - - - +
323C ILE* 1.3 62.5 + - - +
380C ARG* 3.7 7.2 - - - -
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Residues in contact with ILE 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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215C ILE* 6.0 1.3 - - + -
216C TYR* 4.1 26.0 - - + +
235C TYR* 3.3 10.1 - - - -
236C ILE* 2.8 51.3 + - + +
238C VAL* 3.8 28.7 - - + -
267C PHE* 3.7 20.9 - - + -
321C LEU* 4.7 2.7 - - + -
322C TRP* 1.3 80.6 - - - +
324C SER* 1.3 73.3 + - - +
325C LEU 3.5 0.5 + - - -
328C VAL* 4.0 15.5 - - + -
361C VAL* 5.0 6.3 - - + -
368C PHE* 4.1 17.5 - - + -
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Residues in contact with SER 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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234C GLU 3.9 6.4 + - - -
235C TYR* 4.0 12.3 - - - -
266C GLU* 3.2 41.4 + - - +
322C TRP 4.3 0.2 + - - -
323C ILE* 1.3 73.0 - - - +
325C LEU* 1.3 63.0 + - - +
326C ALA* 3.7 9.2 + - - +
327C ALA* 3.7 17.1 + - - +
328C VAL* 2.9 28.3 + - - +
368C PHE* 4.6 0.9 - - - -
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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
------------------------------------------------------------
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