Contacts of the strand formed by residues 241 - 246 (chain A) in PDB entry 2E4H
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 TRP 241 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.6 1.4 - - - +
232A GLY 2.5 46.5 + - - +
234A THR* 3.4 33.7 - - + -
236A PHE* 5.2 1.1 - + - -
237A ALA* 3.2 28.7 - - + +
238A LYS 3.5 16.7 + - - -
239A GLY 3.6 12.1 - - - -
240A GLU* 1.3 84.3 + - - +
242A CYS* 1.3 60.6 + - - +
272A PHE* 3.5 26.2 - - + -
273A ALA* 3.8 1.1 - - - -
274A PRO* 3.6 24.7 - - + -
275A VAL* 4.8 2.8 - - - +
449B GLU* 2.8 38.1 - - + -
450B GLU* 3.9 1.8 - - - -
451B TYR* 4.2 20.9 - + - -
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Residues in contact with CYS 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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212A LEU* 4.8 2.9 - - - -
228A VAL* 3.5 18.8 - - - -
230A PHE 3.5 7.4 - - - -
231A LEU* 3.2 33.9 - - + +
232A GLY 4.6 0.2 - - - +
241A TRP* 1.3 77.1 - - - +
243A GLY* 1.3 73.8 + - - +
244A VAL* 4.1 10.2 + - - +
271A LEU 3.8 0.2 - - - +
272A PHE* 3.2 10.8 - - - +
273A ALA 2.8 41.1 + - - +
274A PRO 4.3 9.0 - - - +
275A VAL* 4.4 4.9 - - + +
278A VAL* 4.6 4.9 - - + -
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Residues in contact with GLY 243 (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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228A VAL* 3.2 5.0 - - - -
229A ARG 2.7 31.7 + - - -
230A PHE 2.6 15.9 + - - +
242A CYS* 1.3 73.6 - - - +
244A VAL* 1.3 59.1 + - - +
263A PHE* 3.4 33.0 - - - -
271A LEU 3.7 2.0 - - - -
272A PHE* 4.7 1.3 - - - -
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Residues in contact with VAL 244 (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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218A VAL* 3.4 24.7 - - + -
220A VAL* 3.3 35.2 - - + -
226A GLY* 3.0 42.0 - - - -
227A VAL 3.0 10.1 - - - +
228A VAL* 4.5 0.7 - - - -
229A ARG* 4.4 1.6 - - - -
242A CYS* 4.2 7.6 - - - +
243A GLY* 1.3 80.8 - - - +
245A GLU* 1.3 60.6 + - - +
246A LEU* 3.4 2.1 + - - +
263A PHE* 4.1 3.2 - - - -
270A GLY* 4.1 0.5 - - - -
271A LEU* 3.0 32.4 + - - +
278A VAL* 4.1 11.2 - - + -
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Residues in contact with GLU 245 (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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226A GLY* 2.7 26.4 - - - -
227A VAL* 2.6 27.6 + - + +
229A ARG* 2.8 40.3 + - + +
244A VAL* 1.3 70.0 - - - +
246A LEU* 1.3 66.5 + - - +
247A ASP* 3.6 1.0 + - - -
263A PHE* 5.2 0.2 - - - -
264A GLN 3.5 1.4 - - - +
265A CYS* 3.5 30.7 - - + +
266A GLN* 4.4 8.5 + - - +
269A TYR* 3.5 13.2 - - + +
270A GLY* 5.1 0.4 - - - -
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Residues in contact with LEU 246 (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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220A VAL* 3.4 33.4 - - + -
224A LYS* 3.6 1.3 - - + -
225A ALA 3.2 8.3 - - - +
245A GLU* 1.3 76.9 - - - +
247A ASP* 1.3 57.5 + - - +
248A GLU 3.3 13.2 - - - +
250A LEU* 3.0 27.6 - - + +
251A GLY* 2.9 45.1 - - - +
268A LYS 4.0 1.1 - - - +
269A TYR* 2.7 54.6 + - - +
271A LEU* 3.6 18.6 - - + -
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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