Contacts of the strand formed by residues 295 - 301 (chain A) in PDB entry 6NFJ
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 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A LYS* 2.9 24.5 + - + +
235A TYR* 3.7 32.3 - + + -
236A TRP* 3.0 29.0 + - - +
284A TYR* 4.3 1.7 - - - -
289A ARG* 4.8 7.4 - - - +
293A LYS 4.1 16.2 - - - -
294A GLY* 1.3 79.0 - - - -
296A LEU* 1.3 63.9 + - - +
368A ASP* 3.3 31.4 - - + -
369A PHE* 3.7 26.0 - + + -
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Residues in contact with LEU 296 (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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193A LEU* 6.2 0.4 - - + -
226A PHE* 3.5 33.2 - - + -
236A TRP* 3.2 25.8 - - + +
237A ILE 5.9 0.2 - - - -
238A THR* 3.7 25.4 - - + -
277A HIS* 4.0 5.4 - - + -
280A VAL* 4.1 6.5 - - + +
281A TRP* 3.8 33.8 - - + -
284A TYR* 3.7 24.7 - - + -
295A TRP* 1.3 77.7 - - - +
297A SER* 1.3 66.7 + - - +
368A ASP* 3.0 31.4 + - - +
369A PHE* 4.2 2.2 - - - -
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Residues in contact with SER 297 (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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236A TRP 3.0 6.5 + - - -
237A ILE* 3.4 6.0 - - - -
238A THR* 3.2 23.9 + - - -
277A HIS* 3.8 11.6 - - - -
296A LEU* 1.3 81.0 - - - +
298A ILE* 1.3 76.9 + - - +
335A HIS* 4.4 0.7 + - - -
367A ALA* 4.0 7.0 - - - +
368A ASP 4.4 0.7 - - - -
369A PHE* 2.6 57.2 + - - -
370A PHE* 4.1 0.5 - - - -
371A ALA 3.7 2.9 + - - -
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Residues in contact with ILE 298 (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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237A ILE* 3.9 4.7 - - - -
238A THR* 3.6 14.8 - - - +
239A ILE* 3.3 21.3 - - + +
242A PRO* 3.9 15.3 - - + -
273A LEU 5.2 2.9 - - - +
274A ILE* 6.2 0.2 - - - -
277A HIS* 3.9 19.7 - - + +
297A SER* 1.3 87.2 + - - +
299A THR* 1.3 63.2 + - - +
300A LEU* 3.4 28.2 + - + +
330A PHE* 5.5 0.9 - - + -
334A ILE* 4.1 26.9 - - + -
335A HIS* 4.1 20.1 - - + -
367A ALA* 5.2 0.2 - - + -
371A ALA* 3.2 22.7 + - - +
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Residues in contact with THR 299 (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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150A GLN* 4.4 1.6 + - - -
237A ILE* 3.3 18.3 - - - +
239A ILE 3.2 12.5 + - - +
240A HIS* 3.4 36.9 + - + +
241A ASN* 2.7 32.3 + - - +
242A PRO* 3.5 4.5 - - - +
298A ILE* 1.3 68.0 - - - +
300A LEU* 1.3 59.8 + - - +
371A ALA* 3.4 16.1 - - - +
372A PHE 4.4 0.4 - - - -
373A SER* 3.9 20.4 - - - +
415A ALA* 3.7 21.3 - - + +
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Residues in contact with LEU 300 (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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242A PRO* 3.7 23.6 - - + -
298A ILE* 3.8 23.8 - - + +
299A THR* 1.3 73.1 - - - +
301A GLY* 1.3 59.5 + - - +
327A LEU* 4.1 14.8 - - + +
330A PHE* 3.6 30.5 - - + +
331A ALA* 3.7 37.0 - - + -
335A HIS* 4.2 16.2 - - + -
371A ALA 3.1 10.1 + - - +
372A PHE* 3.3 14.5 - - + -
373A SER* 3.1 19.2 + - - -
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Residues in contact with GLY 301 (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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241A ASN* 3.2 25.0 + - - +
242A PRO* 5.3 0.2 - - - +
243A TYR* 5.0 2.5 - - - +
299A THR 4.0 0.2 + - - -
300A LEU* 1.3 75.1 - - - +
302A SER* 1.3 62.5 + - - -
326A VAL* 4.1 12.6 - - - +
327A LEU* 3.6 8.5 - - - +
373A SER* 3.6 19.3 - - - -
378A ASN* 3.1 13.8 + - - -
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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