Contacts of the strand formed by residues 282 - 285 (chain A) in PDB entry 4FYT
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 282 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A VAL* 5.1 0.9 - - + -
89A LEU* 3.4 31.4 - - + -
193A PHE* 3.7 13.3 - + + -
209A THR* 3.5 8.3 - - - -
210A THR* 3.1 35.8 + - + +
212A MET* 3.5 19.1 - - + -
220A SER* 3.9 6.5 - - - -
221A PHE* 4.2 12.8 - + - -
235A ILE* 3.5 50.5 - - + -
237A LEU* 3.9 16.4 - - + -
246A LEU 3.6 5.6 - - - -
247A SER* 3.8 0.9 - - - -
280A LEU* 4.2 21.5 - - + -
281A ALA* 1.3 85.6 - - - +
283A ILE* 1.3 66.9 + - - +
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207A VAL* 4.2 14.8 - - + -
208A ALA 3.2 9.4 - - - +
209A THR* 3.5 20.0 - - - +
210A THR* 4.6 2.5 - - - +
237A LEU* 4.1 1.9 - - - +
244A THR 3.6 1.2 - - - +
245A ALA* 3.4 3.3 - - - -
246A LEU* 2.8 47.9 + - + +
281A ALA* 5.1 0.4 - - + -
282A PHE* 1.3 82.0 - - - +
284A VAL* 1.3 70.2 + - - +
285A SER* 4.2 5.4 - - - +
344A ILE* 3.6 48.9 - - + -
346A LEU* 4.6 2.5 - - + -
359A LEU* 3.8 19.7 - - + -
361A THR* 3.9 11.7 - - + -
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A PRO* 4.1 17.9 - - + -
93A LEU* 4.1 9.8 - - + +
193A PHE* 5.2 3.1 - - + -
206A VAL 4.5 1.7 - - - +
207A VAL* 3.5 5.0 - - - +
208A ALA* 2.8 40.8 + - + -
237A LEU* 4.4 16.8 - - + -
239A HIS* 3.8 33.0 - - + -
240A PRO* 4.6 0.7 - - + -
243A LEU* 3.9 24.9 - - + -
244A THR 3.3 5.2 - - - +
245A ALA* 4.5 4.3 - - + -
283A ILE* 1.3 77.5 - - - +
285A SER* 1.3 65.1 + - - +
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A VAL 5.3 1.8 - - - -
207A VAL* 4.1 20.4 - - - +
243A LEU* 3.5 11.0 - - - +
244A THR* 2.8 37.7 + - - +
246A LEU* 5.5 2.6 - - - +
283A ILE* 4.2 9.1 - - - +
284A VAL* 1.3 78.2 - - - +
286A GLU* 1.3 60.9 + - - +
287A PHE* 3.1 38.6 + - - +
303A TRP* 5.3 1.9 - - - -
344A ILE* 4.9 1.7 - - - +
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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
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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