Contacts of the helix formed by residues 289 - 298 (chain T) in PDB entry 3P71
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 PRO 289 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75T HIS* 4.5 9.2 - - + +
79T GLN* 6.3 0.7 - - - +
287T ARG 3.8 2.2 - - - +
288T LEU* 1.4 93.2 - - + +
290T ARG* 1.3 59.8 + - - +
291T ALA* 3.2 4.9 - - + +
292T GLU* 2.8 42.3 + - + +
293T VAL* 3.1 11.1 + - - +
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Residues in contact with ARG 290 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288T LEU 3.4 4.1 + - - +
289T PRO* 1.3 70.7 - - - +
291T ALA* 1.3 57.6 + - - +
293T VAL* 3.4 11.9 + - + +
294T SER* 3.0 31.0 + - - -
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Residues in contact with ALA 291 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289T PRO* 3.1 4.2 + - + -
290T ARG* 1.3 77.6 - - - +
292T GLU* 1.3 61.6 + - + +
294T SER* 3.6 6.6 + - - -
295T ARG* 3.2 21.5 + - - +
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Residues in contact with GLU 292 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71T PHE* 3.9 11.1 - - + -
75T HIS* 4.8 14.6 - - + -
288T LEU* 5.1 2.9 - - + -
289T PRO* 2.8 33.4 + - + +
291T ALA* 1.3 77.4 - - + +
293T VAL* 1.3 66.1 + - + +
295T ARG* 3.1 43.7 + - - +
296T ILE* 3.1 33.3 + - + +
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Residues in contact with VAL 293 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285T TYR* 4.7 15.7 - - + +
286T ASN 6.3 0.2 - - - -
288T LEU* 3.8 31.4 - - + +
289T PRO 3.1 16.1 + - - +
290T ARG* 3.4 11.2 + - + +
292T GLU* 1.3 73.9 - - - +
294T SER* 1.3 57.0 + - - +
296T ILE* 3.4 7.5 + - - +
297T GLU* 2.9 64.1 + - + +
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Residues in contact with SER 294 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290T ARG 3.0 17.9 + - - -
291T ALA* 3.7 8.3 - - - -
292T GLU 3.2 0.2 - - - -
293T VAL* 1.3 76.5 - - - +
295T ARG* 1.3 57.8 + - - +
297T GLU* 4.1 6.8 - - - +
298T SER* 2.9 27.4 + - - -
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Residues in contact with ARG 295 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44T GLY 3.0 26.7 + - - -
45T TYR 2.7 21.8 + - - -
46T TRP* 5.2 0.6 - - - +
71T PHE* 3.4 14.5 - - - -
291T ALA 3.2 11.2 + - - +
292T GLU* 3.1 36.4 + - - +
294T SER* 1.3 75.2 - - - +
296T ILE* 1.3 73.2 + - - +
298T SER* 2.7 20.3 + - - -
299T LEU* 3.5 22.0 + - + +
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Residues in contact with ILE 296 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45T TYR* 3.5 30.3 + - + -
68T ARG* 4.0 22.3 + - + +
71T PHE* 3.0 47.1 - - + -
285T TYR* 4.9 6.3 - - + +
288T LEU* 5.1 4.3 - - + -
292T GLU* 3.1 25.2 + - + +
293T VAL* 3.7 7.2 - - - +
295T ARG* 1.3 88.1 - - - +
297T GLU* 1.3 59.7 + - + +
298T SER 3.0 4.9 - - - -
299T LEU* 2.8 36.9 + - - +
300T GLU 3.7 3.5 + - - +
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Residues in contact with GLU 297 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68T ARG* 3.5 28.9 + - - +
285T TYR* 3.4 20.6 + - - +
293T VAL* 2.9 40.1 + - + +
294T SER* 4.1 5.8 + - - +
296T ILE* 1.3 76.0 - - + +
298T SER* 1.3 55.9 + - - +
299T LEU 3.4 0.4 - - - -
300T GLU 3.3 15.2 - - - +
301T PHE* 5.2 1.2 - - - -
305T MET* 3.6 17.3 - - - +
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Residues in contact with SER 298 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294T SER 2.9 14.0 + - - -
295T ARG* 2.7 23.7 + - - -
297T GLU* 1.3 77.7 - - - +
299T LEU* 1.3 62.6 + - - +
300T GLU 3.6 0.7 - - - -
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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