Contacts of the helix formed by residues 319 - 327 (chain B) in PDB entry 2C1H
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 TYR 319 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B HIS* 5.0 1.6 - - + -
282B TYR* 4.0 8.2 - + + -
286B LYS* 5.1 4.3 - - - -
296B GLU* 4.0 17.1 + - - -
297B ASP* 3.6 14.4 + - - +
300B MET* 3.5 59.5 - - + -
301B MET* 4.5 10.1 - - + -
304B LEU* 4.5 7.4 - - + -
317B THR* 3.0 12.6 + - - +
318B TYR* 1.3 76.5 - - - +
320B ALA* 1.3 54.9 + - - +
321B LYS 3.2 2.9 - - - -
322B GLU* 3.0 38.9 + - + +
323B ALA* 2.8 52.6 + - + +
326B LYS* 3.3 24.3 - - - -
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Residues in contact with ALA 320 (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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36B LEU* 3.8 10.6 - - + +
37B VAL 4.0 4.0 - - - +
38B PHE* 3.8 28.0 - - + +
78B ILE* 3.6 9.2 - - + +
317B THR* 3.1 34.4 + - + +
318B TYR 3.3 1.6 - - - -
319B TYR* 1.3 76.4 - - - +
321B LYS* 1.3 58.3 + - - +
323B ALA* 3.8 4.9 - - - +
324B ALA* 2.9 28.9 + - - +
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Residues in contact with LYS 321 (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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38B PHE* 4.0 13.7 - - + -
69B GLU* 2.7 32.7 + - - +
72B GLU* 3.7 30.3 + - + +
73B LEU* 3.8 22.9 - - + -
76B LEU* 3.6 18.6 - - + -
78B ILE* 4.1 6.5 - - - -
318B TYR 5.9 0.2 - - - +
319B TYR 3.2 1.0 - - - -
320B ALA* 1.3 76.1 - - - +
322B GLU* 1.3 69.8 + - + +
324B ALA* 3.4 1.7 + - - +
325B LYS* 3.1 44.1 + - - +
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Residues in contact with GLU 322 (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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286B LYS* 5.8 4.0 - - - +
296B GLU* 5.4 2.3 - - - +
318B TYR 6.0 0.4 - - - +
319B TYR* 3.0 47.0 + - + +
321B LYS* 1.3 82.2 - - + +
323B ALA* 1.3 62.5 + - - +
325B LYS* 3.3 35.8 + - - +
326B LYS* 3.3 25.5 + - - +
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Residues in contact with ALA 323 (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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36B LEU* 4.0 10.5 - - + -
301B MET* 4.1 12.3 - - - +
304B LEU* 3.8 28.9 - - + -
319B TYR* 2.8 25.5 + - + +
320B ALA* 3.8 4.7 - - - +
322B GLU* 1.3 74.6 - - - +
324B ALA* 1.3 64.5 + - - +
326B LYS* 3.2 4.4 + - - +
327B LEU* 3.1 32.5 + - + +
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Residues in contact with ALA 324 (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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33B VAL* 3.9 23.5 - - + +
36B LEU* 4.1 3.5 - - + +
76B LEU* 4.1 20.7 - - + +
78B ILE* 3.8 23.1 - - + -
320B ALA 2.9 19.8 + - - +
321B LYS 3.6 5.8 - - - +
322B GLU 3.3 0.2 - - - -
323B ALA* 1.3 76.1 - - - +
325B LYS* 1.3 60.6 + - - +
327B LEU 3.3 1.4 + - - -
328B ARG* 3.1 23.7 + - - +
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Residues in contact with LYS 325 (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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72B GLU* 4.5 12.8 + - - -
76B LEU* 3.7 32.1 - - + -
321B LYS* 3.1 33.5 + - - +
322B GLU* 3.5 30.0 + - - +
323B ALA 3.2 0.2 - - - -
324B ALA* 1.3 76.8 - - - +
326B LYS* 1.3 59.7 + - + +
328B ARG* 3.2 48.2 + - - +
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Residues in contact with LYS 326 (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 ASP* 2.7 35.7 + - + +
301B MET* 4.1 28.7 - - + -
319B TYR* 3.3 27.6 - - - +
322B GLU* 3.4 20.1 + - - +
323B ALA 3.2 6.3 + - - +
325B LYS* 1.3 77.5 - - + +
327B LEU* 1.3 61.7 + - - +
328B ARG 3.3 3.1 + - - -
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Residues in contact with LEU 327 (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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31B LEU* 3.4 41.1 - - + +
32B THR* 3.7 27.4 - - - +
33B VAL* 3.9 19.2 - - + +
36B LEU* 4.4 6.5 - - + -
301B MET* 4.3 17.5 - - + -
323B ALA 3.1 23.6 + - - +
324B ALA 3.3 1.1 + - - -
326B LYS* 1.3 76.9 - - - +
328B ARG* 1.3 66.3 + - - +
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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