Contacts of the strand formed by residues 277 - 283 (chain A) in PDB entry 4NJ4
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 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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194A ASP* 3.7 2.7 - - - +
195A TYR* 2.8 43.2 + - + +
219A SER* 2.6 31.9 + - - -
220A PHE 3.7 11.2 - - - +
222A SER* 3.8 16.1 + - - +
224A SER* 3.5 23.4 - - - -
225A ALA 4.8 3.8 + - - -
226A LEU* 5.7 0.4 - - - +
248A VAL* 3.4 16.8 - - - +
268A ILE* 3.5 20.4 - - - +
273A ILE* 3.7 23.1 - - + +
275A GLU 3.2 5.8 + - - +
276A ARG* 1.3 76.9 - - - +
278A ALA* 1.3 64.1 + - - +
279A VAL* 3.9 10.2 - - - +
302A NO3 2.8 41.2 + - - -
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Residues in contact with ALA 278 (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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107A ILE* 4.3 19.7 - - + -
192A ILE* 4.9 2.9 - - + -
193A ASN 3.2 9.6 - - - +
194A ASP* 4.0 10.3 - - + +
219A SER* 3.6 1.0 - - - -
220A PHE* 2.7 36.8 + - - +
221A PHE* 3.5 28.2 - - + -
277A ARG* 1.3 79.3 - - - +
279A VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 279 (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 VAL 3.5 1.9 - - - +
192A ILE* 3.5 3.4 - - - +
193A ASN* 2.9 61.3 + - + +
195A TYR* 3.7 16.2 - - + -
217A SER* 3.7 28.7 - - - +
218A VAL 3.2 12.8 - - - +
277A ARG* 3.9 13.0 - - - +
278A ALA* 1.3 76.2 - - - +
280A ILE* 1.3 64.0 + - - +
281A ILE* 4.0 5.6 - - + -
302A NO3 3.7 23.1 - - - +
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Residues in contact with ILE 280 (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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103A ILE* 4.2 3.4 - - + -
107A ILE* 4.3 7.4 - - + -
167A TRP* 4.1 32.3 - - + -
168A VAL* 4.8 7.0 - - + -
172A VAL* 4.2 12.6 - - + -
190A ALA* 4.7 7.2 - - + -
191A VAL 3.5 7.4 - - - +
192A ILE* 4.1 17.5 - - + -
216A VAL 3.9 0.5 - - - +
217A SER* 3.3 2.1 - - - -
218A VAL* 2.8 47.3 + - + +
220A PHE* 3.7 26.7 - - + -
279A VAL* 1.3 73.4 - - - +
281A ILE* 1.3 63.5 + - - +
282A LEU* 3.9 26.8 + - + +
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Residues in contact with ILE 281 (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 SER 3.6 1.9 - - - +
190A ALA* 3.4 4.7 - - - -
191A VAL* 2.8 41.7 + - + +
193A ASN* 3.0 31.2 - - - +
195A TYR* 5.7 0.2 - - - +
206A ASP* 4.8 1.1 - - - +
215A ILE* 4.3 9.9 - - + -
216A VAL 3.4 9.2 - - - +
217A SER* 4.3 5.6 - - - -
279A VAL* 4.0 15.0 - - + -
280A ILE* 1.3 73.1 - - - +
282A LEU* 1.3 61.8 + - - +
283A ARG* 3.5 45.1 + - + +
302A NO3 4.4 11.7 - - - +
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Residues in contact with LEU 282 (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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168A VAL* 4.2 4.3 - - + -
172A VAL* 3.8 19.1 - - + -
173A ILE* 4.1 17.5 - - + -
176A LEU* 3.4 32.1 - - + -
186A PHE* 5.0 1.0 - - - -
187A VAL* 3.9 26.5 - - + +
189A SER 3.4 1.8 - - - -
190A ALA* 3.8 26.7 - - + -
214A PRO 4.6 1.0 - - - +
215A ILE* 4.5 0.3 - - - -
216A VAL* 2.8 44.0 + - + +
218A VAL* 4.1 9.0 - - + -
280A ILE* 3.9 17.3 - - + +
281A ILE* 1.3 72.7 - - - +
283A ARG* 1.3 62.4 + - - +
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Residues in contact with ARG 283 (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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139A TYR* 3.8 19.4 + - - -
186A PHE* 4.5 5.4 - - - -
187A VAL* 3.6 5.7 - - - +
188A ASN* 3.0 7.5 + - - +
189A SER* 2.9 37.6 + - - +
191A VAL* 3.4 34.2 - - - +
206A ASP* 3.0 34.7 + - - -
211A PHE* 3.5 54.9 - - + -
212A GLU 5.3 0.7 - - - +
214A PRO 5.0 0.7 - - - +
215A ILE* 3.9 20.4 - - + -
281A ILE* 3.5 29.2 + - + +
282A LEU* 1.3 79.3 - - - +
284A LYS* 1.3 60.8 + - - +
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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