Contacts of the helix formed by residues 317 - 325 (chain A) in PDB entry 2OT7
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 MET 317 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A MET* 3.9 13.9 - - + -
296A TRP* 3.4 43.1 - - + -
297A ILE* 3.4 37.7 - - + +
300A GLY* 3.8 21.5 - - - +
301A LYS* 3.9 9.6 - - + +
315A ILE* 3.3 9.8 + - - +
316A SER* 1.3 72.7 + - - +
318A ASP* 1.3 64.1 + - - +
319A VAL 3.2 2.9 - - - -
320A PHE* 2.9 24.9 + - + +
321A VAL* 3.0 12.2 + - + +
332A TRP* 3.9 22.1 - - + -
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Residues in contact with ASP 318 (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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316A SER* 3.3 15.2 - - - +
317A MET* 1.3 76.7 - - - +
319A VAL* 1.3 63.7 + - - +
321A VAL 4.0 0.2 - - - -
322A ARG* 3.1 45.5 + - - +
329A TYR* 2.8 29.5 + - - -
332A TRP* 3.7 14.9 - - + -
333A LYS* 2.4 40.2 + - - -
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU* 3.7 22.8 - - + +
160A VAL* 5.5 2.2 - - + -
163A GLU* 3.5 37.2 - - + +
316A SER* 4.2 7.9 + - - +
318A ASP* 1.3 79.2 - - - +
320A PHE* 1.3 93.4 + - + +
322A ARG* 3.7 23.1 + - - +
323A LYS* 3.3 24.2 + - + +
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Residues in contact with PHE 320 (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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156A ILE* 3.3 39.0 - - + -
157A LEU* 4.4 5.4 - - + -
159A LEU* 3.6 26.5 - - + -
160A VAL* 3.9 25.1 - - + -
296A TRP* 3.8 33.9 - + - -
297A ILE* 3.9 29.5 - - + +
315A ILE* 4.2 5.2 - - + -
316A SER 4.0 8.5 - - - -
317A MET* 2.9 13.5 + - + +
319A VAL* 1.3 99.5 - - + +
321A VAL* 1.3 60.6 + - - +
324A PHE* 3.0 38.7 + + - +
325A GLN 3.9 0.2 + - - -
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Residues in contact with VAL 321 (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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297A ILE* 4.5 3.4 - - + -
301A LYS* 3.7 31.4 - - + +
317A MET* 3.0 16.0 + - + +
318A ASP 4.2 0.7 - - - +
320A PHE* 1.3 77.0 - - - +
322A ARG* 1.3 57.7 + - - +
325A GLN* 2.9 64.3 + - + +
328A ARG 4.5 0.9 - - - -
329A TYR* 3.9 24.9 - - + +
332A TRP* 4.0 32.8 - - + -
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Residues in contact with ARG 322 (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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318A ASP* 3.1 36.0 + - - +
319A VAL* 3.9 29.9 + - - +
321A VAL* 1.3 77.9 - - - +
323A LYS* 1.3 61.8 + - - +
326A PRO* 3.6 21.6 - - - +
329A TYR* 3.8 35.9 + - + -
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Residues in contact with LYS 323 (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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159A LEU* 4.2 23.6 - - + +
163A GLU* 5.8 0.8 + - - -
319A VAL* 3.3 16.0 + - + +
322A ARG* 1.3 82.2 - - - +
324A PHE* 1.3 96.1 + - + +
326A PRO* 3.8 7.1 - - - +
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Residues in contact with PHE 324 (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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156A ILE* 3.9 28.9 - - + -
159A LEU* 3.5 26.5 - - + -
294A ARG* 3.8 37.2 + - + +
297A ILE* 3.6 24.2 - - + -
320A PHE* 3.0 19.6 + + - +
323A LYS* 1.3 104.7 - - + +
325A GLN* 1.3 64.9 + - + +
326A PRO* 3.4 7.4 - - - +
327A GLU* 4.4 3.6 - - - +
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Residues in contact with GLN 325 (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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294A ARG 5.5 1.0 + - - -
297A ILE* 3.7 30.7 - - + +
298A GLU* 3.3 23.6 + - - +
301A LYS* 2.7 30.2 + - - +
321A VAL* 2.9 25.1 + - + +
324A PHE* 1.3 86.6 - - + +
326A PRO* 1.3 60.4 - - - +
327A GLU* 3.2 17.9 - - - +
328A ARG* 3.0 29.3 + - + +
329A TYR 3.3 8.1 + - - -
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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