Contacts of the strand formed by residues 261 - 266 (chain C) in PDB entry 5FI6
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 GLY 261 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C TYR* 4.5 0.2 - - - -
260C TRP* 1.3 76.7 - - - +
262C VAL* 1.3 64.6 + - - +
274C THR 3.6 7.0 - - - -
276C ASP 3.6 12.8 + - - -
277C THR* 3.9 5.6 - - - -
423C CYS* 3.4 14.0 - - - -
499C CYS* 3.3 5.0 - - - -
500C TRP* 2.8 39.2 + - - +
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Residues in contact with VAL 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C ILE* 4.1 16.8 - - + +
234C TYR* 4.4 8.7 - - + -
260C TRP* 3.3 40.6 - - + -
261C GLY* 1.3 73.7 - - - +
263C SER* 1.3 66.0 + - - +
264C VAL* 5.3 0.3 - - - +
272C HIS 4.3 0.3 - - - +
273C SER* 3.4 1.6 - - - -
274C THR* 2.9 36.1 + - - +
277C THR* 3.4 1.3 - - - +
497C MET* 3.4 27.4 - - + -
498C MET 3.5 3.1 - - - -
499C CYS* 4.0 10.3 - - - -
516C PHE* 3.7 19.1 - - + -
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Residues in contact with SER 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C VAL* 1.3 71.1 - - - +
264C VAL* 1.3 62.7 + - - +
272C HIS 3.5 3.8 - - - -
273C SER* 3.2 5.7 + - - -
277C THR* 3.2 13.2 - - - -
423C CYS* 3.2 26.6 - - - +
424C GLU* 3.1 35.0 + - - +
427C SER* 3.5 5.4 - - - -
497C MET* 3.2 29.3 - - - +
498C MET 3.1 8.5 + - - -
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Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C PHE* 4.5 5.2 - - + -
226C PHE* 4.3 9.6 - - + -
230C ILE* 4.2 31.9 - - + -
262C VAL* 4.7 0.4 - - + +
263C SER* 1.3 80.3 - - - +
265C CYS* 1.3 69.0 + - - +
266C THR* 4.4 9.2 - - + -
270C GLN 4.0 0.4 - - - -
271C ARG* 3.3 8.3 + - - +
272C HIS* 2.7 47.5 + - + +
273C SER* 5.3 0.2 + - - -
427C SER* 4.1 2.5 + - - -
495C MET* 3.7 27.8 - - + -
496C GLY 3.8 2.2 - - - -
497C MET* 3.9 17.9 - - + -
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Residues in contact with CYS 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C VAL* 1.3 74.7 - - - +
266C THR* 1.3 67.5 + - - +
269C GLY* 4.4 1.8 - - - -
270C GLN 3.3 4.9 - - - -
271C ARG* 3.8 23.1 - - - +
427C SER* 3.7 24.7 + - - +
428C VAL* 4.1 13.0 - - + -
431C ALA* 3.2 20.7 - - - +
440C PRO* 4.0 11.9 - - - -
441C ILE* 4.2 6.3 - - - -
495C MET* 4.0 1.3 - - - -
496C GLY 2.8 34.5 + - - -
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Residues in contact with THR 266 (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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219C VAL* 3.9 3.8 - - - -
220C ILE* 4.5 11.0 - - + -
223C PHE* 3.6 32.5 - - + -
264C VAL* 4.4 4.0 - - + -
265C CYS* 1.3 78.7 - - - +
267C VAL* 1.3 62.4 + - - +
268C ASP 2.9 10.6 + - - -
269C GLY 3.1 8.5 + - - -
270C GLN* 2.7 46.2 + - - +
431C ALA* 4.5 1.3 - - - -
440C PRO* 3.3 12.5 - - - +
494C VAL 3.4 11.7 - - - +
495C MET* 3.6 13.0 - - + -
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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
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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