Contacts of the strand formed by residues 310 - 317 (chain C) in PDB entry 5Y7K
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 ARG 310 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305C TRP* 3.5 3.9 - - - -
306C ALA* 2.8 42.4 + - + -
307C THR* 3.1 27.5 + - - +
308C GLN 3.7 0.2 - - - -
309C GLU* 1.3 79.5 - - - +
311C ILE* 1.3 57.1 + - - +
327C ILE* 3.6 23.6 - - + -
328C CYS 3.3 4.0 - - - +
329C ASP* 2.9 35.9 + - - +
337C TRP* 4.1 0.2 - - - -
343C ARG* 3.4 15.0 - - - +
364C PHE* 5.2 0.2 - - - -
367C ASP 4.0 3.8 + - - -
368C GLY* 2.4 42.3 + - - -
369C ASN* 3.1 23.0 + - - -
389C ILE* 3.1 12.3 - - - +
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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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224C ALA* 3.7 16.6 - - + -
268C PHE* 3.8 16.8 - - + -
270C VAL* 5.0 1.3 - - + -
287C ILE* 4.1 22.2 - - + -
303C VAL* 3.8 8.5 - - + -
304C THR 3.7 12.1 - - - +
305C TRP* 3.6 45.3 - - + +
310C ARG* 1.3 76.6 - - - +
312C SER* 1.3 64.1 + - - +
313C LEU* 3.9 8.6 + - + -
326C ASP 4.0 0.5 - - - +
327C ILE* 4.8 0.2 - - - -
328C CYS* 2.9 39.1 + - + +
337C TRP* 4.0 14.1 - - + -
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Residues in contact with SER 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302C ASP* 4.5 1.7 + - - +
303C VAL* 3.6 0.3 - - - -
304C THR* 2.6 55.6 + - - +
306C ALA* 4.7 1.0 - - - +
311C ILE* 1.3 71.4 - - - +
313C LEU* 1.3 69.7 + - - +
325C MET* 4.6 13.0 - - - +
326C ASP 3.2 9.4 - - - -
327C ILE* 4.5 3.4 - - - +
362C PRO* 3.8 4.0 - - - +
364C PHE* 3.3 36.6 - - - -
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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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268C PHE* 3.6 42.6 - - + -
287C ILE* 4.1 17.7 - - + -
300C LEU* 4.1 10.1 - - + -
302C ASP 3.7 5.2 - - - +
303C VAL* 4.5 3.8 - - + -
311C ILE* 3.9 23.3 - - + +
312C SER* 1.3 81.3 - - - +
314C GLN* 1.3 62.0 + - - +
315C TRP* 3.6 39.5 - - + +
325C MET* 3.1 6.8 - - - +
326C ASP* 2.7 42.2 + - + +
328C CYS* 5.2 2.2 - - - -
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Residues in contact with GLN 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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300C LEU* 3.6 8.1 - - - +
301C CYS* 3.2 29.8 + - - -
302C ASP* 3.2 43.7 + - + +
312C SER 5.8 0.2 - - - -
313C LEU* 1.3 79.2 - - - +
315C TRP* 1.3 64.3 + - - +
323C SER* 3.8 7.3 + - - +
324C VAL 3.4 4.3 - - - +
325C MET* 3.8 22.0 - - + +
347C GLU* 4.1 1.4 - - - +
359C PRO* 3.2 24.2 - - - +
360C SER 2.7 26.3 + - - -
362C PRO* 3.7 9.3 - - - +
373C LYS* 3.3 15.7 + - - +
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Residues in contact with TRP 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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266C VAL* 3.9 28.9 - - + -
267C LYS* 5.4 0.7 - - - -
268C PHE* 4.4 15.5 - - + -
287C ILE* 4.5 4.2 - - - +
288C THR 4.5 3.3 + - - -
289C ALA* 3.4 36.7 - - + +
290C PRO* 3.5 22.2 - - + +
293C MET* 3.3 23.3 - - + +
298C HIS* 3.7 11.9 - + + -
299C TYR 3.4 20.0 - - - -
300C LEU* 3.8 20.2 - - + -
301C CYS* 4.2 1.3 - - - -
313C LEU* 3.6 36.5 - - + +
314C GLN* 1.3 78.4 - - - +
316C LEU* 1.3 61.1 + - - +
323C SER* 3.1 8.9 + - - -
324C VAL 2.8 39.1 + - - +
326C ASP* 4.6 7.2 + - + +
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Residues in contact with LEU 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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293C MET* 3.8 3.6 - - - -
298C HIS* 3.1 1.6 - - - -
299C TYR* 2.6 49.8 + - + +
301C CYS* 4.1 15.0 - - + -
315C TRP* 1.3 74.5 - - - +
317C ARG* 1.3 67.4 + - - +
320C GLN* 3.5 54.3 - - + +
322C TYR 3.2 19.7 - - - +
354C VAL* 3.8 17.5 - - + +
357C PHE 6.0 0.2 - - - +
358C ARG* 5.5 3.1 - - + -
359C PRO* 4.3 28.3 - - + -
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Residues in contact with ARG 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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292C SER* 3.3 33.4 + - - +
293C MET* 3.6 18.5 - - - +
295C ILE* 4.9 9.2 - - + +
297C ASP 3.8 7.9 - - - +
298C HIS* 4.1 2.2 - - + +
299C TYR* 4.1 1.6 - - - -
316C LEU* 1.3 77.6 - - - +
318C ARG* 1.3 68.5 + - - +
319C ILE* 3.2 26.2 + - + +
320C GLN* 3.5 11.1 + - - +
321C ASN* 5.7 0.4 - - - -
322C TYR* 3.3 63.2 + - - +
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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