Contacts of the strand formed by residues 309 - 313 (chain C) in PDB entry 3CQ6
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C ASN* 3.4 37.5 - - - +
171C ASN 3.2 21.3 - - - -
172C ASN* 3.7 11.0 - - + -
173C PRO* 3.3 29.8 - - + -
174C THR 4.4 0.2 - - - -
175C GLY* 3.8 5.6 - - - -
200C TYR* 3.7 17.0 - + - -
288C ARG* 4.6 0.7 - - - +
305C SER* 2.8 26.7 + - - -
307C SER* 3.2 27.7 + - - +
308C ASN* 1.3 87.6 - - - +
310C VAL* 1.3 67.5 + - - +
311C PHE 4.9 0.4 - - - -
342C ARG* 3.6 18.6 - - + -
343C THR 3.1 16.6 - - - +
344C THR* 4.1 0.2 - - - +
345C ILE* 4.2 3.7 - - - +
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Residues in contact with VAL 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C ARG* 4.0 22.0 - - + -
291C VAL* 4.6 4.9 - - + -
292C ALA* 4.5 12.3 - - + -
295C LEU* 4.2 15.7 - - + -
302C VAL* 3.4 32.8 - - + -
303C VAL 4.5 3.1 - - - +
305C SER* 4.8 5.6 - - - -
309C PHE* 1.3 79.9 - - - +
311C PHE* 1.3 67.0 + - - +
312C PHE* 3.7 1.8 - - + -
341C LEU 3.7 0.9 - - - +
342C ARG* 3.4 6.1 - - - -
343C THR* 2.8 45.2 + - + +
345C ILE* 4.1 13.9 - - + -
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Residues in contact with PHE 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PRO* 5.5 0.2 - - + -
146C PHE* 3.8 28.5 - + - -
173C PRO* 3.3 42.8 + - + +
174C THR* 4.1 21.6 + - + +
303C VAL* 2.9 57.1 + - + -
305C SER* 5.5 0.4 - - - -
309C PHE* 4.4 1.2 - - - -
310C VAL* 1.3 74.5 - - - +
312C PHE* 1.3 63.6 + - - +
335C VAL* 3.9 13.7 - - + -
337C ILE* 4.0 21.5 - - + -
340C HIS* 3.4 29.2 - + + -
341C LEU 3.5 15.3 - - - -
342C ARG* 4.3 2.9 - - + -
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Residues in contact with PHE 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C LEU* 4.1 22.7 - - + -
300C TYR* 3.7 31.6 - + + -
301C ALA 3.1 12.8 - - - +
302C VAL* 4.3 7.6 - - + -
310C VAL* 3.7 10.3 - - + -
311C PHE* 1.3 76.9 - - - +
313C GLY* 1.3 57.0 + - - +
315C PHE* 3.8 22.1 - + - -
325C PHE* 4.1 9.9 - + - -
332C ILE* 4.0 13.0 - - + -
340C HIS* 3.1 8.6 - - - -
341C LEU* 2.9 57.0 + - + -
343C THR* 4.1 12.1 - - + -
354C PHE* 3.8 32.1 - + - -
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Residues in contact with GLY 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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300C TYR* 3.6 19.5 - - - -
301C ALA 2.8 30.3 + - - -
312C PHE* 1.3 73.8 - - - +
314C ASP* 1.3 64.1 + - - -
315C PHE* 4.1 6.7 - - - -
339C GLY 3.0 11.9 - - - -
340C HIS* 3.6 9.0 - - - -
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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