Contacts of the strand formed by residues 299 - 304 (chain v) in PDB entry 6FF7
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 299 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239v PRO* 5.3 12.3 - - + -
243v ASP* 6.6 0.2 - - + -
293v HIS 3.3 13.2 - - - +
294v LYS* 4.3 9.6 - - + -
295v THR 4.9 0.2 - - - +
298v MET* 1.3 81.2 - - - +
300v PHE* 1.3 63.6 + - - +
314v THR* 4.4 2.6 - - - -
315v LEU* 4.3 18.2 + - - +
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Residues in contact with PHE 300 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291v ALA 4.7 0.2 - - - -
292v THR* 3.7 2.6 - - - -
293v HIS* 2.9 37.3 + - + +
299v PHE* 1.3 75.4 - - - +
301v PHE* 1.3 65.1 + - - +
302v LEU 4.3 0.2 - - - -
312v LYS* 5.8 2.7 - - + -
313v ILE 3.3 16.2 - - - +
314v THR* 4.6 7.6 - - - -
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Residues in contact with PHE 301 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290v SER 3.9 11.2 - - - +
291v ALA 3.5 6.3 - - - +
292v THR* 4.9 4.7 - - - -
300v PHE* 1.3 77.4 - - - +
302v LEU* 1.3 60.3 + - - +
303v ALA* 3.3 5.4 + - + +
311v PHE 2.9 4.7 - - - +
312v LYS* 3.7 2.4 - - - -
313v ILE* 2.9 46.7 + - + +
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Residues in contact with LEU 302 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289v CYS* 5.0 1.9 - - - +
290v SER 3.4 3.0 - - - -
291v ALA* 3.0 35.7 + - + +
293v HIS* 6.1 0.4 - - - +
301v PHE* 1.3 67.9 - - - +
303v ALA* 1.3 65.9 + - - +
304v GLN* 3.9 3.1 + - - +
310v ILE* 5.4 8.0 - - + +
311v PHE 3.5 6.7 - - - +
312v LYS* 5.1 1.1 - - - +
339v MET* 5.2 1.6 - - - +
341v VAL* 5.6 6.5 - - + -
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Residues in contact with ALA 303 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287v PHE* 5.4 5.6 - - + -
289v CYS 3.7 12.6 - - - +
290v SER* 3.7 11.0 - - - +
301v PHE* 3.3 7.5 + - + +
302v LEU* 1.3 78.4 - - - +
304v GLN* 1.3 60.4 + - - +
309v ASP 4.7 0.2 - - - -
310v ILE* 3.2 5.5 - - - +
311v PHE* 2.8 43.7 + - + +
313v ILE* 5.5 4.7 - - + -
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Residues in contact with GLN 304 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287v PHE* 3.3 6.1 - - - +
288v VAL* 2.7 33.6 + - + -
289v CYS* 3.4 25.2 + - + +
302v LEU 4.8 2.0 - - - +
303v ALA* 1.3 77.2 - - - +
305v THR* 1.3 59.6 + - - +
308v GLY* 5.5 4.5 - - - -
309v ASP 3.8 7.2 - - - +
310v ILE* 5.1 4.0 - - + -
336v ALA* 5.4 8.7 - - + +
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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