Contacts of the strand formed by residues 422 - 428 (chain B) in PDB entry 2EIT
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 VAL 422 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B LYS* 5.5 0.3 + - - -
314B ALA* 5.1 1.9 + - - -
315B TYR* 4.2 0.8 - - - -
325B ALA 5.0 1.1 - - - +
326B SER* 3.9 21.0 - - - +
372B VAL* 3.9 27.8 - - + -
376B ILE* 4.2 15.7 - - + +
402B THR* 3.6 8.1 - - + -
404B PHE* 3.9 32.3 - - + -
413B ILE* 5.8 0.7 - - + -
418B ILE* 3.8 37.8 - - + +
420B GLY 2.8 12.8 + - - +
421B PRO* 1.3 80.2 - - + +
423B LEU* 1.3 62.3 + - - +
424B SER* 4.1 2.6 + - - +
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Residues in contact with LEU 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B VAL* 3.9 24.9 - - + -
314B ALA* 4.2 8.5 - - + -
315B TYR* 3.6 23.1 + - + +
325B ALA* 3.6 24.9 - - + +
326B SER* 3.7 14.6 - - - +
327B ARG 3.8 14.8 - - - +
328B LEU* 3.9 19.5 - - + +
342B VAL* 4.3 13.5 - - + -
402B THR 3.0 7.4 + - - +
403B VAL* 3.5 5.2 - - + +
404B PHE* 2.9 29.3 + - - +
422B VAL* 1.3 73.4 - - - +
424B SER* 1.3 61.4 + - - +
425B VAL* 4.3 7.6 - - + -
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Residues in contact with SER 424 (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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326B SER 2.9 14.9 + - - -
327B ARG* 3.3 7.2 - - - +
328B LEU 2.7 31.4 + - - +
404B PHE* 3.6 5.2 - - - +
407B VAL* 3.9 19.7 - - - -
413B ILE* 3.1 41.4 + - - +
414B ALA* 4.8 4.7 - - - -
418B ILE* 5.3 0.7 - - - +
422B VAL* 5.0 3.8 + - - +
423B LEU* 1.3 73.9 + - - +
425B VAL* 1.3 56.1 + - - +
426B ILE* 4.0 3.2 + - - +
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Residues in contact with VAL 425 (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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328B LEU* 3.4 25.8 - - + +
330B LEU* 3.9 26.7 - - + -
335B TYR* 3.9 17.2 - - + +
339B LEU* 4.1 16.4 - - + -
342B VAL* 6.0 0.2 - - + -
403B VAL* 3.7 22.4 - - + -
404B PHE 2.8 20.2 + - - +
405B THR* 4.2 6.1 - - + -
406B GLU 3.4 8.5 + - - -
407B VAL* 3.3 23.3 + - - +
423B LEU* 4.3 5.6 - - + -
424B SER* 1.3 75.8 - - - +
426B ILE* 1.3 62.9 + - - +
427B ARG 4.3 0.3 + - - -
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Residues in contact with ILE 426 (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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327B ARG* 4.2 24.5 - - + +
328B LEU 2.8 12.4 + - - +
329B ILE* 3.4 8.3 - - + +
330B LEU* 2.9 26.9 + - - +
335B TYR* 4.8 3.1 - - - -
407B VAL* 3.5 26.7 - - + +
409B PRO* 3.9 26.0 - - + +
414B ALA* 4.0 24.5 - - + -
424B SER* 4.4 5.6 - - - +
425B VAL* 1.3 77.2 - - - +
427B ARG* 1.3 70.2 + - - +
428B VAL* 3.9 5.5 + - + -
437B VAL* 4.0 25.4 - - + -
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Residues in contact with ARG 427 (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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330B LEU 3.5 5.4 - - - +
332B GLN* 4.6 18.5 + - + +
335B TYR* 3.2 64.3 - - + +
336B GLU* 4.0 9.9 + - - +
406B GLU* 3.5 31.5 + - - +
407B VAL 5.1 0.4 + - - -
409B PRO* 6.0 0.3 - - - +
425B VAL 4.3 0.6 + - - -
426B ILE* 1.3 76.6 - - - +
428B VAL* 1.3 72.5 + - - +
433B GLU* 4.9 0.7 - - - +
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Residues in contact with VAL 428 (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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329B ILE* 3.8 17.9 - - + -
330B LEU 2.9 21.3 + - - +
331B THR* 3.3 5.3 - - - -
332B GLN* 2.9 29.0 + - - +
409B PRO* 5.9 0.2 - - + -
426B ILE* 4.2 6.3 - - + -
427B ARG* 1.3 81.0 - - - +
429B LYS* 1.3 60.9 + - - +
430B ASP 3.7 17.7 - - - +
433B GLU* 3.5 18.8 - - + +
434B ALA* 3.7 17.3 - - + -
437B VAL* 3.8 29.4 - - + -
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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