Contacts of the strand formed by residues 309 - 317 (chain C) in PDB entry 3DHW
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 PHE 309 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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201C MET* 4.4 15.9 - - + -
205C LYS* 3.9 22.9 - - + -
225C VAL* 4.1 21.1 - - + -
226C SER* 5.8 0.2 - - - -
228C VAL* 3.2 28.7 - - + -
229C PHE* 3.9 17.3 - + - -
237C ALA* 4.5 26.5 - - - +
239C LYS 6.2 1.1 - - - -
272C GLU* 6.2 0.2 - - - -
301C MET* 3.2 25.7 - - - +
302C ASP* 2.6 20.1 + - + +
304C ALA* 3.1 38.8 - - + -
307C VAL* 3.5 3.3 + - + -
308C LYS* 1.3 75.9 - - - +
310C GLY* 1.3 59.0 + - - +
311C ILE* 5.6 2.5 - - + -
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Residues in contact with GLY 310 (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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272C GLU* 3.2 17.6 + - - +
273C PHE* 3.3 27.8 + - - +
300C GLN 3.4 9.4 - - - -
301C MET* 4.0 9.2 - - - -
308C LYS* 3.7 2.7 + - - -
309C PHE* 1.3 77.3 - - - +
311C ILE* 1.3 72.8 + - - +
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Residues in contact with ILE 311 (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 ALA 5.8 0.7 - - - +
238C GLN* 4.5 29.6 - - + +
241C ILE* 3.6 21.5 - - + -
244C THR* 3.0 33.0 - - + +
270C ARG* 4.7 9.4 - - - +
271C LEU 3.3 4.7 - - - +
272C GLU* 3.5 31.0 - - + +
273C PHE* 4.6 1.9 - - - -
299C ALA* 3.6 0.7 - - - -
300C GLN 3.2 40.4 + - - +
301C MET* 5.9 0.2 - - - +
309C PHE* 5.6 2.0 - - + -
310C GLY* 1.3 81.7 - - - +
312C MET* 1.3 72.2 + - - +
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Residues in contact with MET 312 (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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244C THR* 5.4 2.6 - - - +
269C LEU 3.4 0.2 - - - +
270C ARG* 3.0 9.5 - - - +
271C LEU* 2.7 49.2 + - + +
273C PHE* 3.7 24.5 - - + -
283C LEU* 3.4 32.5 - - + -
296C ILE* 4.0 3.6 - - + -
298C SER 3.4 17.3 - - - +
299C ALA* 3.6 21.5 - - + +
300C GLN 5.3 0.7 - - - +
301C MET* 5.0 8.3 - - + -
311C ILE* 1.3 84.6 - - - +
313C LEU* 1.3 64.0 + - - +
314C THR* 3.6 15.3 - - + -
296D ILE* 4.9 20.2 - - + +
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Residues in contact with LEU 313 (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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238C GLN* 6.1 0.9 - - - +
244C THR* 4.1 19.7 - - + +
245C LEU* 5.7 1.1 - - + -
247C LEU* 3.5 28.3 - - + -
248C ASP* 3.9 15.5 - - - +
268C MET* 5.1 5.4 - - + -
269C LEU 3.5 0.9 - - - +
270C ARG* 3.0 44.2 - - + -
297C ILE* 2.9 17.0 + - + +
298C SER* 2.7 37.8 + - - -
312C MET* 1.3 73.5 - - - +
314C THR* 1.3 55.7 + - - +
340C LEU* 3.3 24.2 - - + -
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Residues in contact with THR 314 (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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268C MET* 2.9 10.6 - - - +
269C LEU* 2.5 51.9 + - - +
271C LEU* 4.4 12.2 - - + +
283C LEU* 5.0 2.7 - - + +
294C ASN* 5.1 6.1 + - - +
295C ASN 3.2 10.5 - - - -
296C ILE* 3.3 39.3 - - + -
297C ILE* 4.0 2.7 - - - +
312C MET* 3.6 16.4 - - + -
313C LEU* 1.3 76.4 - - - +
315C GLU* 1.3 67.4 + - - +
316C MET* 5.2 4.2 - - - +
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Residues in contact with GLU 315 (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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253C TYR* 2.9 27.5 + - - +
256C ARG* 5.7 2.6 + - - -
266C VAL* 4.2 6.1 - - + -
267C PRO 3.3 7.4 - - - +
268C MET* 5.1 2.0 - - - -
294C ASN* 3.6 3.5 - - - -
295C ASN* 2.8 60.1 + - + +
297C ILE* 4.2 9.0 - - + -
314C THR* 1.3 79.1 + - - +
316C MET* 1.3 60.9 + - - +
317C HIS* 3.2 15.8 + - - +
343C VAL* 3.8 27.6 - - + +
278D VAL* 4.2 17.2 - - - +
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Residues in contact with MET 316 (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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266C VAL* 3.0 19.8 - - - +
267C PRO* 3.2 14.8 + - + +
269C LEU* 4.2 25.3 - - + +
271C LEU* 5.3 2.0 - - + -
283C LEU* 4.4 13.5 - - + -
286C THR* 5.3 2.0 - - - +
292C VAL* 4.1 14.4 - - + -
293C ASN 3.4 1.8 - - - -
294C ASN* 3.4 23.6 - - - +
314C THR* 4.4 4.7 + - - +
315C GLU* 1.3 75.0 - - - +
317C HIS* 1.3 57.9 + - - +
323C THR* 3.4 29.5 - - + +
326C ALA* 3.2 34.5 - - + -
327C ILE* 4.5 7.9 - - + -
330C LEU* 4.6 12.3 - - + -
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Residues in contact with HIS 317 (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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266C VAL* 3.5 29.3 - - + +
291C ASN 4.3 0.3 - - - +
292C VAL* 3.3 8.0 - - - +
293C ASN* 2.7 58.6 + - + +
295C ASN* 3.4 26.8 + - - -
315C GLU* 3.2 25.0 + - + -
316C MET* 1.3 72.5 - - - +
318C GLY* 1.3 58.5 + - - +
323C THR* 4.4 1.3 - - - -
343C VAL* 5.8 1.1 - - + -
278D VAL* 5.7 2.0 - - - +
279D ASP* 4.7 15.1 + - + -
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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