Contacts of the strand formed by residues 319 - 322 (chain L) in PDB entry 2FRV
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 ILE 319 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314L PHE* 4.2 17.3 - - + -
316L PRO* 3.6 33.9 - - + +
317L ASP 3.3 2.1 - - - +
318L LEU* 1.3 77.8 - - - +
320L GLU* 1.3 71.1 + - - +
321L GLU* 4.9 1.6 - - + +
335L HIS* 3.2 26.7 - - - -
336L PRO* 3.7 24.7 - - + -
360L PRO* 5.3 0.4 - - + -
361L ARG 3.7 4.5 - - - -
362L TYR* 4.2 10.8 - - + -
465L MET* 5.0 7.4 - - + -
467L SER* 5.3 1.6 - - - +
469L TRP* 4.2 11.2 - - + -
483L VAL* 4.9 11.2 - - + -
488L TRP* 4.1 28.3 - - + -
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Residues in contact with GLU 320 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317L ASP 5.9 0.9 - - - +
318L LEU 3.9 3.8 + - - +
319L ILE* 1.3 79.2 - - - +
321L GLU* 1.3 58.1 + - - +
322L HIS* 4.6 5.6 - - - +
333L ALA* 2.5 52.0 - - + +
334L HIS* 2.6 11.7 + - - -
335L HIS* 3.5 14.7 + - + +
360L PRO* 3.5 1.0 - - - +
361L ARG* 2.8 39.6 + - + +
364L GLY 6.3 0.7 - - - +
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Residues in contact with GLU 321 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319L ILE* 5.0 3.8 - - + -
320L GLU* 1.3 73.1 - - - +
322L HIS* 1.3 64.0 + - - +
323L VAL* 4.7 2.8 - - - +
332L GLY 3.8 2.1 - - - +
333L ALA* 3.0 18.6 - - - -
334L HIS* 3.2 18.2 + - + +
336L PRO* 4.9 5.2 - - + +
339L GLY* 5.8 0.9 - - - -
358L LYS* 4.0 31.5 + - + +
359L ALA 3.7 4.0 - - - -
360L PRO* 3.8 20.8 - - + +
481L GLN* 3.9 19.1 + - - -
482L LEU 4.0 5.0 - - - +
483L VAL* 3.3 42.2 - - + +
487L THR* 4.1 5.5 - - - +
540L MG 4.0 7.4 - - - -
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Residues in contact with HIS 322 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320L GLU* 4.2 5.8 - - - +
321L GLU* 1.3 72.5 - - - +
323L VAL* 1.3 71.5 + - - +
324L LYS 4.4 1.8 - - - +
326L SER* 3.9 1.0 + - - -
331L ALA 5.1 1.2 + - - -
333L ALA* 3.4 28.3 + - + +
358L LYS* 3.6 5.5 - - - +
359L ALA* 2.8 52.6 + - + +
361L ARG* 3.6 29.6 - - + +
364L GLY* 5.7 2.6 - - - -
494L CYS* 3.6 15.0 - - + -
495L ALA* 3.3 35.2 + - + +
496L GLU* 5.0 8.5 - - - -
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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