Contacts of the strand formed by residues 238 - 242 (chain A) in PDB entry 2FE5
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 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229A LEU* 4.8 0.7 - - + -
236A LEU* 3.9 28.8 - - + +
237A GLY* 1.3 77.6 - - - +
239A SER* 1.3 63.4 + - - +
240A ILE* 3.8 24.4 + - + +
257A ILE* 3.9 27.8 - - + -
259A LYS 3.2 14.6 - - - +
260A ILE* 4.1 14.1 - - + -
261A ILE* 3.9 4.6 - - - +
266A ALA* 4.0 8.7 - - + -
272A LEU* 4.0 7.4 - - + -
278A LEU* 4.5 6.5 - - + -
298A LEU* 3.8 32.9 - - + +
307A LEU* 3.8 28.3 - - + -
401A GOL 4.9 3.4 + - - -
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Residues in contact with SER 239 (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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238A PHE* 1.3 74.4 - - - +
240A ILE* 1.3 65.1 + - - +
257A ILE* 3.4 8.5 - - - +
258A THR* 2.9 36.3 + - - -
259A LYS* 3.0 29.4 + - - +
261A ILE* 3.8 12.0 - - - +
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Residues in contact with ILE 240 (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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238A PHE* 3.8 26.0 - - + +
239A SER* 1.3 80.0 - - - +
241A ALA* 1.3 57.0 + - - +
255A ILE* 3.7 22.4 - - + -
256A TYR 3.2 12.1 - - - +
257A ILE* 4.3 3.8 - - + -
258A THR* 4.1 4.0 - - - -
278A LEU* 4.5 2.9 - - + -
291A HIS* 2.8 32.1 + - + +
294A ALA* 3.7 30.3 - - + -
295A VAL* 3.9 19.1 - - + +
298A LEU* 3.8 22.2 - - + -
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Residues in contact with ALA 241 (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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240A ILE* 1.3 76.0 - - - +
242A GLY* 1.3 66.1 + - - +
246A ASN* 4.5 4.5 - - - +
248A HIS* 4.5 11.0 - - - +
255A ILE* 3.4 8.7 - - - +
256A TYR* 2.9 29.0 + - - +
258A THR* 3.6 23.3 - - + +
291A HIS* 3.9 6.7 - - - -
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Residues in contact with GLY 242 (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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241A ALA* 1.3 79.3 - - - +
243A GLY* 1.3 58.0 + - - -
246A ASN* 3.0 40.9 + - - +
248A HIS* 4.1 15.6 - - - +
254A SER 3.4 11.9 - - - -
255A ILE* 3.8 2.4 - - - +
291A HIS* 3.3 15.8 - - - +
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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