Contacts of the strand formed by residues 201 - 208 (chain A) in PDB entry 4N41
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 201 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A ARG* 4.3 7.6 - - + -
193A VAL 3.5 11.7 - - - +
194A ARG* 4.4 7.8 + - - +
199A ARG 3.4 9.2 + - - -
200A ARG* 1.3 78.9 + - - +
202A TRP* 1.3 86.1 + - - +
246A ASP* 5.4 3.5 - - - +
247A PRO* 5.4 3.1 - - - +
264A VAL* 4.1 17.0 - - + +
10C A 3.9 24.6 + - - +
11C G 3.2 28.6 + - - +
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Residues in contact with TRP 202 (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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192A ARG* 3.3 9.4 - - - +
193A VAL* 2.8 40.8 + - + +
195A ASN* 3.1 37.7 + - - +
200A ARG* 4.6 7.7 + - + +
201A THR* 1.3 84.1 - - - +
203A GLU* 1.3 59.4 + - - +
244A VAL* 3.7 30.5 - - + -
245A ALA 3.4 24.2 - - - +
246A ASP* 3.6 33.9 - - + -
247A PRO 5.8 0.7 - - - -
254A ILE* 4.0 22.7 - - + -
256A HIS* 3.9 11.8 + + - -
261A LEU* 4.5 6.3 - - + -
20C G 4.3 19.1 - - - -
21C T 4.2 16.8 - - - -
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Residues in contact with GLU 203 (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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191A LYS 3.4 11.7 - - - +
192A ARG* 4.4 6.7 - - + +
202A TRP* 1.3 71.0 - - - +
204A LEU* 1.3 64.5 + - - +
205A LEU* 3.2 3.0 + - - -
245A ALA* 2.9 50.1 + - + +
246A ASP 5.8 0.2 - - - -
247A PRO* 5.5 5.8 - - + -
250A PRO* 6.5 0.9 - - + -
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Residues in contact with LEU 204 (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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179A LEU* 4.5 15.7 - - + -
189A LEU* 3.8 33.2 - - + +
190A PRO* 3.4 35.3 - - + +
191A LYS* 3.0 15.3 + - - +
193A VAL* 4.0 17.2 - - + +
202A TRP 3.8 3.8 + - - -
203A GLU* 1.3 67.3 - - - +
205A LEU* 1.3 61.5 + - - +
206A ARG* 3.8 14.8 - - - +
207A LEU* 5.7 1.3 - - + -
242A ALA* 3.9 19.3 - - + -
243A TRP 3.2 19.7 - - - +
244A VAL* 4.2 7.9 - - + -
261A LEU* 5.3 1.3 - - + -
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Residues in contact with LEU 205 (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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189A LEU* 5.2 3.9 - - - +
203A GLU 3.2 6.6 + - - +
204A LEU* 1.3 75.7 - - - +
206A ARG* 1.3 66.5 + - + +
243A TRP* 2.9 23.2 + - + +
244A VAL* 4.6 5.6 - - - +
245A ALA* 5.1 5.2 - - + -
253A PRO* 5.9 6.3 - - + -
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Residues in contact with ARG 206 (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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189A LEU* 4.7 12.6 - - + -
204A LEU* 3.7 8.3 - - - +
205A LEU* 1.3 84.0 - - + +
207A LEU* 1.3 66.2 + - - +
242A ALA* 3.5 2.8 - - - -
243A TRP* 2.6 44.3 + - + +
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Residues in contact with LEU 207 (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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179A LEU* 4.7 2.0 - - + -
183A LEU* 4.0 26.7 - - + -
189A LEU* 4.2 20.3 - - + +
204A LEU* 5.7 1.3 - - + -
206A ARG* 1.3 80.8 - - - +
208A GLY* 1.3 58.4 + - - +
240A ARG* 5.3 5.2 - - + -
241A VAL 3.6 15.5 - - - +
242A ALA* 4.5 6.5 - - + -
243A TRP* 3.4 13.3 - - - -
258A THR* 4.1 19.7 - - + -
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Residues in contact with GLY 208 (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 LEU* 1.3 77.0 - - - +
209A GLU* 1.3 57.8 + - - -
210A GLU* 3.0 12.7 + - - +
240A ARG* 4.8 4.0 - - - +
241A VAL* 3.0 41.0 + - - +
243A TRP* 4.3 14.1 - - - -
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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