Contacts of the strand formed by residues 198 - 201 (chain B) in PDB entry 7CE1
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 ARG 198 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196B ARG 3.5 0.4 - - - -
197B LYS* 1.3 82.0 - - - +
199B ILE* 1.3 60.4 + - - +
228B SER* 3.4 5.4 - - - +
230B PHE* 4.6 7.2 - - + +
257B ARG 4.8 1.6 - - - +
258B PRO* 3.5 14.6 - - + -
259B ASP* 3.0 20.1 + - + +
260B GLY* 2.4 37.1 + - - +
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Residues in contact with ILE 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 5.2 13.7 - - + -
191B LEU* 4.0 36.3 - - + -
196B ARG 3.7 21.5 - - - +
198B ARG* 1.3 84.2 - - - +
200B ALA* 1.3 65.5 + - - +
218B PHE* 3.3 31.9 - - + -
222B ILE* 5.7 1.8 - - + -
227B VAL* 4.0 14.1 - - + +
228B SER 3.0 20.2 + - - +
229B GLU* 3.1 8.5 - - + +
230B PHE* 2.3 37.2 + - - +
260B GLY* 3.2 4.3 - - - -
262B VAL* 4.5 0.4 - - + -
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199B ILE* 1.3 75.4 - - - +
201B ILE* 1.3 62.3 + - - +
218B PHE* 3.9 5.1 - - - -
230B PHE* 4.0 5.6 - - + -
232B LEU* 3.8 30.3 - - + -
258B PRO* 4.5 9.9 - - + -
260B GLY 3.0 11.7 + - - +
261B ILE* 3.5 21.5 - - + -
262B VAL* 2.9 28.1 + - - +
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Residues in contact with ILE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200B ALA* 1.3 75.9 - - - +
202B ILE* 1.3 70.6 + - - +
203B VAL* 3.5 34.1 + - + +
214B ALA* 4.3 4.3 - - + +
215B ARG* 4.3 12.3 - - + -
218B PHE* 3.3 49.8 - - + -
229B GLU* 3.7 22.4 - - + +
230B PHE 4.8 1.2 + - - -
231B PRO 4.9 8.3 - - - +
232B LEU* 4.1 16.3 - - - +
235B ILE 5.2 1.9 - - - +
262B VAL* 3.7 6.1 - - + +
264B ILE* 5.8 2.9 - - + -
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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