Contacts of the strand formed by residues 313 - 318 (chain C) in PDB entry 3COG
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 MET 313 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164C GLN* 3.2 22.0 + - - +
190C PHE* 3.8 28.9 - - + -
213C TYR* 3.6 19.3 - - + +
291C TYR* 3.2 22.7 - - - -
311C THR* 3.3 17.2 - - + +
312C GLY* 1.3 75.9 - - - +
314C VAL* 1.3 57.9 + - - +
341C LEU* 3.6 31.4 - - + -
375C ARG* 3.5 34.5 - - - +
376C LEU 3.5 13.7 - - - +
377C SER* 3.7 20.0 - - - -
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Residues in contact with VAL 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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164C GLN* 3.9 0.7 - - - +
273C GLY* 3.6 24.5 - - - +
276C VAL* 4.1 5.8 - - + -
277C ALA* 4.0 18.4 - - + -
280C LEU* 3.9 26.5 - - + -
289C VAL* 4.1 6.1 - - + -
290C ILE 4.3 3.6 - - - +
291C TYR* 3.9 10.8 - - + -
312C GLY 3.8 10.1 - - - +
313C MET* 1.3 78.8 - - - +
315C THR* 1.3 70.0 + - - +
316C PHE* 4.8 0.2 - - - -
375C ARG* 3.7 0.8 - - - -
376C LEU* 2.8 46.9 + - + +
378C VAL* 4.0 10.3 - - + -
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Residues in contact with THR 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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162C PRO 2.7 29.3 + - - +
164C GLN* 3.0 16.7 + - - +
289C VAL* 3.6 4.0 - - - +
290C ILE* 2.7 56.0 + - + +
314C VAL* 1.3 74.7 - - - +
316C PHE* 1.3 64.9 + - - +
317C TYR* 5.3 0.2 - - + -
373C LEU* 3.7 30.1 - - + -
374C ILE 3.4 11.7 - - - +
375C ARG* 3.9 9.1 - - - +
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Residues in contact with PHE 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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280C LEU* 3.7 23.6 - - + -
286C VAL* 3.9 21.8 - - + -
288C LYS 3.2 13.7 - - - +
289C VAL* 4.0 13.7 - - + +
290C ILE 4.5 0.7 - - - +
314C VAL 4.8 0.2 - - - -
315C THR* 1.3 81.5 - - - +
317C TYR* 1.3 75.2 + - - +
318C ILE* 4.1 11.9 - - + -
328C PHE* 4.0 18.2 - + - -
372C THR 3.7 0.3 - - - +
373C LEU* 3.5 3.5 - - - +
374C ILE* 2.8 81.2 + - + +
376C LEU* 4.1 22.2 - - + -
394C LEU* 4.5 5.2 - - + -
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Residues in contact with TYR 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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163C THR* 4.8 3.3 - - - +
286C VAL 3.7 1.0 - - - -
287C GLU* 2.8 39.5 + - + +
288C LYS* 2.8 36.1 + - + +
290C ILE* 3.9 26.0 - - + +
316C PHE* 1.3 82.3 - - - +
318C ILE* 1.3 62.8 + - - +
367C LEU 5.0 0.2 + - - -
368C GLY* 2.6 30.8 + - - -
370C SER* 3.3 27.8 - - - -
372C THR* 3.4 13.2 - - - +
373C LEU* 3.6 23.8 - - + +
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Residues in contact with ILE 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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285C TRP 3.8 13.0 - - - +
287C GLU* 4.3 3.8 - - - +
316C PHE* 3.9 8.4 - - + -
317C TYR* 1.3 75.3 - - - +
319C LYS* 1.3 75.7 + - - +
320C GLY 3.9 0.5 + - - +
321C THR 4.5 0.2 - - - +
324C HIS* 3.6 25.6 - - + +
325C ALA* 3.9 22.9 - - + +
328C PHE* 3.7 20.9 - - + -
372C THR* 3.1 39.6 + - + +
374C ILE* 4.0 9.4 - - + -
394C LEU* 4.0 18.4 - - + -
397C ALA* 4.2 8.7 - - + -
399C PRO* 4.2 3.4 - - + -
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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