Contacts of the strand formed by residues 306 - 318 (chain C) in PDB entry 3C6M
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 LEU 306 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269C GLU* 3.9 8.3 - - - +
270C PHE 3.5 15.5 - - - +
271C ASP 3.8 3.6 - - - +
273C VAL* 3.9 17.0 - - + +
302C SER 3.1 14.2 + - - +
303C MET* 3.1 37.8 + - + +
305C VAL* 1.3 79.9 - - - +
307C LYS* 1.3 69.2 + - - +
308C GLN 3.6 0.3 + - - -
310C GLY* 4.0 9.2 - - - +
311C LYS* 3.6 28.3 - - - +
312C TYR* 4.0 14.6 - - + +
360C VAL 4.5 2.7 - - - +
361C TRP* 4.9 4.3 - - - -
362C LYS* 2.8 33.7 + - + +
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Residues in contact with LYS 307 (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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193C ASP* 5.9 2.9 - - - -
269C GLU* 4.0 34.5 - - + +
270C PHE 2.9 22.5 + - - +
271C ASP* 3.2 29.8 + - - +
305C VAL 3.9 1.2 + - - -
306C LEU* 1.3 83.2 - - - +
308C GLN* 1.3 61.3 + - - +
309C ASP* 3.2 2.7 - - + +
310C GLY* 2.9 25.9 + - - +
362C LYS* 4.4 1.4 - - - +
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Residues in contact with GLN 308 (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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269C GLU* 5.1 2.0 + - - -
306C LEU 3.6 1.6 + - - -
307C LYS* 1.3 71.7 - - - +
309C ASP* 1.3 73.1 + - - +
310C GLY 3.3 2.1 + - - +
361C TRP* 5.8 0.3 - - - +
362C LYS* 3.5 49.4 + - - +
363C LYS 3.3 24.9 + - - +
364C ALA* 3.8 11.1 - - - +
365C LYS* 3.9 32.8 + - + +
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Residues in contact with ASP 309 (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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307C LYS* 3.2 3.9 - - + +
308C GLN* 1.3 89.2 + - - +
310C GLY* 1.3 63.6 + - - +
311C LYS* 5.0 5.0 - - - +
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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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271C ASP* 3.0 22.0 - - - -
272C TYR* 5.6 0.7 - - - -
306C LEU* 4.0 12.5 - - - +
307C LYS* 2.9 18.6 + - - +
308C GLN 3.3 1.9 - - - +
309C ASP* 1.3 83.0 - - - +
311C LYS* 1.3 65.7 + - - +
361C TRP* 3.8 15.6 - - - +
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Residues in contact with LYS 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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187C GLU* 3.4 35.6 + - - +
271C ASP 3.0 6.5 + - - -
272C TYR* 3.1 43.2 - - + +
273C VAL 3.2 3.8 + - - +
306C LEU* 3.6 5.3 - - - +
309C ASP 5.0 3.6 - - - +
310C GLY* 1.3 80.1 - - - +
312C TYR* 1.3 60.4 + - - +
313C PHE* 4.2 16.4 + - + -
359C THR* 4.4 14.6 - - + +
360C VAL 3.8 6.7 - - - +
361C TRP* 4.7 15.7 - - + -
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Residues in contact with TYR 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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273C VAL* 3.1 30.1 - - + +
275C ASN* 2.8 45.0 + - + +
298C ILE* 4.6 1.4 - - - +
299C LEU* 3.5 29.4 - - + +
302C SER* 3.5 30.9 + - - -
303C MET* 3.4 24.0 - - + -
306C LEU* 4.0 4.0 - - + +
311C LYS* 1.3 73.8 - - - +
313C PHE* 1.3 63.4 + - - +
314C THR* 3.9 23.1 - - + +
328C TYR* 4.3 1.6 + - - -
359C THR* 3.4 4.7 - - - +
360C VAL* 2.8 54.4 + - + +
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Residues in contact with PHE 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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180C ALA 4.7 3.1 - - - -
181C ILE* 3.0 31.4 - - + +
182C MET 3.9 3.6 - - - -
183C GLY* 3.5 28.0 - - - -
187C GLU* 3.7 15.3 - - + -
189C TYR* 3.7 21.5 - - - -
272C TYR* 3.9 22.0 - + - -
273C VAL 2.9 6.3 + - - +
274C ILE* 3.4 13.4 - - + +
275C ASN* 2.7 33.3 + - - +
311C LYS* 4.2 16.2 - - + -
312C TYR* 1.3 79.1 - - - +
314C THR* 1.3 57.4 + - - +
358C TYR 3.5 4.9 - - - +
359C THR* 3.2 35.9 - - + -
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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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181C ILE* 3.7 9.9 - - - +
275C ASN* 2.9 37.2 + - - +
312C TYR* 3.9 10.3 - - + +
313C PHE* 1.3 77.7 - - - +
315C GLN* 1.3 78.8 + - - +
328C TYR* 3.4 29.8 - - + +
357C PHE* 3.5 9.0 - - - +
358C TYR* 2.9 45.0 + - + +
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Residues in contact with GLN 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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177C TYR* 3.3 36.1 - - + +
181C ILE* 3.6 4.2 - - - +
275C ASN* 4.7 4.0 - - - +
277C LEU 4.0 10.0 - - - +
278C THR 4.6 0.5 - - - +
279C ALA* 4.0 13.9 - - - +
314C THR* 1.3 90.8 + - - +
316C GLY* 1.3 74.4 + - - +
328C TYR* 5.7 1.6 - - - -
355C TRP* 2.7 50.9 - - - +
356C VAL 4.0 0.2 - - - -
357C PHE* 4.0 10.5 - - + -
501C SPM 3.5 23.9 - - + +
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Residues in contact with GLY 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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314C THR* 4.0 2.1 + - - -
315C GLN* 1.3 87.4 + - - +
317C ASN* 1.3 66.7 + - - +
325C LEU* 4.5 2.2 - - - -
328C TYR* 5.5 5.4 - - - -
355C TRP* 4.7 0.2 - - - -
356C VAL 2.7 18.8 + - - -
358C TYR* 3.7 25.7 - - - -
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Residues in contact with ASN 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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127C ALA* 4.2 2.8 - - - +
279C ALA* 6.6 0.4 - - - -
292C TRP* 5.8 1.6 - - - -
316C GLY* 1.3 77.2 + - - +
318C CYS* 1.3 77.2 + - - +
321C LEU* 3.4 25.6 - - + +
324C ALA* 3.7 25.3 - - - +
325C LEU* 3.9 20.9 - - + +
355C TRP* 3.5 26.4 - - - +
356C VAL* 2.9 28.9 + - - +
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Residues in contact with CYS 318 (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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127C ALA* 4.0 1.6 - - - -
128C ASP* 3.9 16.2 - - - -
317C ASN* 1.3 81.8 + - - +
319C VAL* 1.3 68.8 + - + +
320C ASN* 2.8 6.1 + - - -
321C LEU* 2.9 48.6 + - - +
325C LEU* 4.0 5.2 - - - +
353C GLU* 3.3 29.2 - - + +
354C LEU 3.4 10.8 - - - +
355C TRP* 3.5 19.3 - - + -
356C VAL* 4.4 0.4 - - - -
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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