Contacts of the strand formed by residues 314 - 318 (chain B) in PDB entry 5F6K
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 SER 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ALA* 3.6 11.9 - - - -
297B GLN* 3.4 33.1 - - - +
298B LEU* 3.2 29.5 - - - +
310B GLU 4.5 2.1 + - - -
312B GLY 3.3 4.8 + - - -
313B TYR* 1.3 74.8 - - - +
315B MET* 1.3 60.9 + - - +
353B LEU 3.4 7.2 - - - -
354B GLN* 4.7 0.7 - - - -
355B ALA 4.2 1.6 - - - -
472B ILE 3.8 0.7 - - - +
473B SER* 3.2 20.5 - - - -
474B LEU 3.2 10.5 + - - +
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Residues in contact with MET 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ALA* 3.0 25.5 + - - +
298B LEU* 3.5 3.3 - - - +
314B SER* 1.3 75.4 - - - +
316B VAL* 1.3 70.5 + - - +
317B ARG* 3.9 25.4 - - - -
347B SER* 4.1 4.7 - - - +
351B GLY 4.7 3.6 - - - -
352B ASN 3.1 21.5 - - - +
353B LEU* 2.8 29.2 + - + +
355B ALA 3.7 11.4 - - - +
356B PRO 4.1 2.9 - - - +
357B LEU* 3.5 42.0 - - + -
360B ASP* 6.2 0.2 - - - +
363B SER* 4.9 3.6 - - - +
471B ALA* 4.3 5.4 - - + -
472B ILE 3.2 15.3 - - - +
473B SER* 4.2 2.2 - - - +
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Residues in contact with VAL 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 4.2 18.1 - - + +
290B ALA 4.3 2.7 - - - +
293B ASP 4.1 3.8 - - - +
294B ARG* 3.6 21.3 - - + -
298B LEU* 3.8 17.5 - - + -
300B ILE* 3.7 17.7 - - + -
307B VAL* 4.3 16.2 - - + -
315B MET* 1.3 75.0 - - - +
317B ARG* 1.3 76.7 + - - +
353B LEU* 4.8 0.2 - - - -
471B ALA* 3.5 2.1 - - - +
472B ILE* 2.8 54.3 + - + +
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Residues in contact with ARG 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B LEU* 3.8 4.1 - - - -
290B ALA* 2.8 27.1 + - - +
293B ASP* 2.7 54.5 + - - +
315B MET* 3.9 5.2 - - - -
316B VAL* 1.3 80.6 - - - +
318B ALA* 1.3 64.7 + - - +
347B SER* 3.4 13.2 + - - -
348B GLN 3.3 22.4 + - - -
349B PRO* 3.0 26.6 + - - +
351B GLY* 2.8 28.5 + - - -
353B LEU* 3.5 17.9 - - + +
469B PHE* 3.9 22.9 - - + -
470B PRO 3.4 3.8 - - - +
471B ALA* 4.0 20.0 - - + -
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B VAL* 4.9 2.2 - - + -
288B LEU 3.3 12.1 - - - +
289B LEU* 4.3 3.5 - - + +
290B ALA* 4.0 5.6 - - - +
293B ASP* 4.7 1.7 - - - +
317B ARG* 1.3 81.1 - - - +
319B SER* 1.3 64.1 + - - +
320B HIS 3.3 5.4 - - - +
469B PHE* 3.4 15.4 - - - +
470B PRO* 2.8 34.3 + - + +
484B PHE* 3.7 27.8 - - + -
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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