Contacts of the strand formed by residues 239 - 243 (chain A) in PDB entry 4GWR
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 THR 239 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL 3.7 1.2 - - - +
185A PHE* 2.8 37.5 + - - +
234A ILE* 4.0 15.9 - - + +
235A ARG 5.1 1.0 + - - -
236A GLY 2.5 29.0 + - - -
237A PHE* 4.0 0.2 - - - +
238A PRO* 1.3 74.5 + - - +
240A ILE* 1.3 62.3 + - - +
241A LYS* 3.8 35.2 - - + -
251A ASP* 4.4 9.2 - - - +
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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
----------------------------------------------------------
182A MET* 4.7 6.1 - - + -
183A VAL 3.3 12.8 - - - +
184A GLU* 4.0 20.6 - - + -
196A LEU* 4.4 18.8 - - + -
200A TRP* 3.7 38.8 - - + -
238A PRO* 5.4 3.1 - - + -
239A THR* 1.3 75.5 - - - +
241A LYS* 1.3 65.2 + - - +
242A ILE* 5.0 1.3 - - + -
251A ASP* 3.6 7.6 - - - +
252A TYR* 3.0 64.7 + - + +
256A ARG* 5.3 7.6 - - + +
261A ILE* 5.9 0.4 - - + -
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Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A MET* 3.6 1.0 - - - -
183A VAL 2.8 31.6 + - - -
185A PHE* 4.1 12.1 - - + -
232A TYR* 3.5 32.0 + - + +
233A GLY 5.6 1.1 + - - -
234A ILE* 3.9 6.3 - - - -
239A THR* 3.8 20.9 - - + -
240A ILE* 1.3 75.5 - - - +
242A ILE* 1.3 64.2 + - - +
243A PHE* 3.7 23.5 - - + -
249A PRO* 3.9 28.3 + - + +
250A VAL 3.4 3.6 - - - +
251A ASP* 2.7 30.6 + - - +
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Residues in contact with ILE 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A VAL* 4.1 5.2 - - + -
181A TRP 3.4 7.2 - - - +
182A MET* 4.2 17.3 - - + -
240A ILE* 5.0 0.7 - - + -
241A LYS* 1.3 77.8 - - - +
243A PHE* 1.3 64.5 + - - +
244A GLN* 4.1 4.5 + - + +
248A SER 4.4 0.5 - - - +
249A PRO* 3.1 5.4 - - - +
250A VAL* 2.7 46.9 + - + +
251A ASP 4.8 0.4 - - - +
252A TYR* 4.2 24.9 - - + +
264A ARG* 3.4 45.5 - - + +
268A LEU* 3.6 32.3 - - + -
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Residues in contact with PHE 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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170A PHE* 3.5 22.7 - + - -
174A VAL* 3.6 26.0 - - + +
175A LEU* 4.3 11.2 - - + -
179A ASP 4.4 1.4 - - - +
180A VAL* 3.5 6.1 - - - +
181A TRP* 2.8 34.1 + - + +
183A VAL* 3.8 22.2 - - + -
185A PHE* 4.3 3.4 - + - -
232A TYR* 3.5 32.3 - + - -
241A LYS* 3.7 29.8 - - + -
242A ILE* 1.3 75.4 - - - +
244A GLN* 1.3 64.6 + - - +
247A GLU 5.0 4.5 - - - -
249A PRO* 3.5 35.9 - - + -
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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
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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