Contacts of the strand formed by residues 361 - 367 (chain B) in PDB entry 4EVI
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 361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU* 3.5 22.6 - - - +
17A TRP* 3.6 18.7 - - - -
182B ASP* 2.7 45.6 + - - -
186B PHE* 3.6 25.0 - - + -
267B LYS* 3.8 9.1 - - - +
268B TRP* 3.5 36.4 - - - +
301B ALA 5.2 1.1 - - - -
302B ASP* 3.4 18.6 - - - +
303B HIS* 3.6 17.3 - - + +
309B SER* 5.0 1.0 + - - -
356B PRO* 5.2 0.2 - - - +
357B VAL* 3.2 5.5 + - - -
358B GLY* 3.0 28.6 + - - +
359B GLY* 3.0 16.6 + - - +
360B LEU* 1.3 81.9 - - - +
362B VAL* 1.3 68.5 + - - +
403B GOL 3.7 2.3 + - - -
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Residues in contact with VAL 362 (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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186B PHE* 4.5 1.8 - - - -
300B ILE 3.6 0.5 - - - +
301B ALA* 3.4 5.4 - - - +
302B ASP 2.9 35.3 + - - +
304B VAL* 3.5 33.0 - - + +
307B HIS* 4.0 16.2 - - + +
309B SER* 3.8 21.5 - - - +
310B CYS* 5.6 1.3 - - - -
354B ILE* 3.7 16.8 - - + -
355B THR 3.6 10.5 - - - +
356B PRO* 3.9 8.1 - - + -
357B VAL* 3.9 9.9 - - - +
360B LEU 5.4 1.3 - - - +
361B ARG* 1.3 81.4 - - - +
363B LEU* 1.3 60.8 + - - +
364B ILE* 4.1 9.2 - - + -
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Residues in contact with LEU 363 (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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190B LEU* 4.2 17.0 - - + -
194B CYS* 3.7 26.2 - - + -
197B ALA* 3.6 31.6 - - + -
265B LEU* 5.0 2.0 - - + -
299B MET* 3.9 24.7 - - + -
300B ILE 3.4 22.9 - - - +
301B ALA* 4.5 4.5 - - + +
353B LYS 3.6 0.9 - - - +
354B ILE* 3.3 4.9 - - - +
355B THR* 2.8 44.3 + - - +
357B VAL* 3.8 0.6 - - - +
362B VAL* 1.3 73.4 - - - +
364B ILE* 1.3 71.6 + - - +
365B GLU* 3.9 9.9 - - + +
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Residues in contact with ILE 364 (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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298B LEU 3.6 0.7 - - - +
299B MET* 3.4 4.0 - - - -
300B ILE* 2.7 55.8 + - + +
302B ASP* 5.9 1.3 - - + +
303B HIS 5.5 0.2 - - - +
304B VAL* 3.8 22.7 - - + -
340B TRP* 4.0 28.9 - - + +
344B PHE* 3.7 19.3 - - + -
352B TYR* 4.1 18.6 - - + -
353B LYS 3.4 4.3 - - - +
354B ILE* 4.2 7.6 - - + -
362B VAL* 4.1 13.7 - - + -
363B LEU* 1.3 76.3 - - - +
365B GLU* 1.3 61.8 + - - +
366B VAL* 3.6 21.6 + - + +
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Residues in contact with GLU 365 (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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197B ALA* 3.5 20.9 + - + +
297B LYS* 2.7 37.8 + - + +
298B LEU 3.4 6.3 - - - +
299B MET* 4.9 3.4 - - + -
352B TYR* 3.1 5.5 - - - +
353B LYS* 2.8 53.9 + - - +
355B THR* 4.4 8.8 + - - -
363B LEU* 3.9 19.1 - - + +
364B ILE* 1.3 72.0 - - - +
366B VAL* 1.3 59.7 + - - +
367B TYR* 3.6 29.1 + - + +
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Residues in contact with VAL 366 (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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297B LYS* 3.7 4.0 - - - +
298B LEU* 2.8 53.8 + - + +
300B ILE* 4.5 1.3 - - + -
344B PHE* 3.7 36.8 - - + -
349B PHE* 3.5 33.9 - - + -
351B ASP 3.6 8.3 - - - +
352B TYR* 4.1 0.7 - - + -
364B ILE* 3.6 27.1 - - + +
365B GLU* 1.3 78.8 - - - +
367B TYR* 1.3 65.1 + - - +
368B PRO* 3.9 1.6 - - - +
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Residues in contact with TYR 367 (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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295B LYS* 6.2 0.7 - - + -
296B GLY 5.6 0.7 - - - -
297B LYS* 4.4 26.9 - - + -
349B PHE* 3.6 4.1 - - - +
350B LYS* 2.8 26.5 + - + +
351B ASP* 2.8 49.2 + - + +
352B TYR* 4.0 7.0 - - - -
353B LYS* 3.7 20.6 - - + +
365B GLU* 3.6 37.3 + - + +
366B VAL* 1.3 75.4 - - - +
368B PRO* 1.3 70.4 - - + +
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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