Contacts of the helix formed by residues 304 - 313 (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 GLU 304 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ASP* 5.4 0.9 - - - +
59C HIS* 5.5 1.4 + - - -
89C ARG* 4.6 4.3 + - - +
118C HIS* 5.2 5.4 + - - -
214C ARG* 3.5 18.5 + - - +
241C HIS 3.7 12.6 - - - +
243C LEU* 4.7 8.6 + - - +
260C PHE* 5.4 2.4 - - - -
265C TYR* 2.7 40.2 + - - -
302T LEU* 3.3 15.2 - - + +
303T ASP* 1.3 98.3 + - - +
305T MET* 1.3 63.8 - - - +
306T GLU* 3.2 19.6 - - - +
307T LEU* 3.1 34.9 + - + +
308T LEU 4.0 0.9 + - - -
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Residues in contact with MET 305 (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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213C PRO 5.5 6.1 - - - +
68T ARG* 3.4 29.6 - - - +
282T MET* 5.5 6.6 - - + +
285T TYR* 4.2 11.4 - - + +
297T GLU* 3.6 18.4 - - - +
302T LEU* 4.2 17.9 - - - +
303T ASP 3.8 2.4 + - - -
304T GLU* 1.3 72.2 - - - +
306T GLU* 1.3 62.8 + - - +
307T LEU 3.1 0.2 - - - -
308T LEU* 3.2 23.3 + - - +
309T GLU* 2.9 28.5 + - - +
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Residues in contact with GLU 306 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C ARG* 4.9 7.4 + - - -
242C GLN* 5.2 6.2 - - - +
243C LEU* 4.6 35.6 + - + +
303T ASP 4.5 1.2 - - - +
304T GLU* 3.2 21.3 - - + +
305T MET* 1.3 84.5 + - - +
307T LEU* 1.3 61.0 + - + +
309T GLU* 3.6 10.8 - - + +
310T GLN* 3.0 28.6 + - - +
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Residues in contact with LEU 307 (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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89C ARG* 3.4 35.9 - - - +
243C LEU* 4.3 11.9 - - + -
265C TYR* 3.7 18.6 - - + -
266C CYS* 4.0 7.6 - - - -
268C ARG* 5.0 5.2 - - - +
269C CYS* 3.6 31.2 - - - -
65T GLU* 4.8 11.0 - - + +
304T GLU* 3.1 34.9 + - + +
306T GLU* 1.3 77.6 - - + +
308T LEU* 1.3 65.8 + - - +
310T GLN* 3.6 6.3 + - - +
311T LEU* 3.2 27.7 + - - +
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Residues in contact with LEU 308 (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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308C PHE* 5.3 1.3 - - + -
65T GLU* 3.6 34.8 - - + +
68T ARG* 4.0 25.6 - - + -
69T GLY 4.3 5.2 - - - +
282T MET* 4.6 4.5 - - + -
285T TYR* 4.0 24.5 - - + -
302T LEU* 4.1 14.4 - - + -
304T GLU 4.0 0.6 + - - -
305T MET* 3.2 24.5 + - - +
307T LEU* 1.3 77.6 - - - +
309T GLU* 1.3 55.6 + - - +
311T LEU* 3.0 5.7 + - + +
312T MET* 2.8 66.9 + - + +
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Residues in contact with GLU 309 (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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282T MET* 3.2 38.7 - - + +
286T ASN* 5.0 0.9 + - - -
305T MET 2.9 17.7 + - - +
306T GLU* 3.6 11.0 - - + +
308T LEU* 1.3 76.1 - - - +
310T GLN* 1.3 63.4 + - - +
312T MET* 4.2 0.3 - - - +
313T ARG* 3.1 62.8 + - + +
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Residues in contact with GLN 310 (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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243C LEU* 5.4 3.0 - - - +
245C MET* 4.4 13.5 - - - +
269C CYS* 3.1 47.9 + - - +
237T PHE* 3.4 36.7 - - + +
306T GLU 3.0 18.7 + - - +
307T LEU* 4.0 6.2 - - - +
308T LEU 3.3 0.2 - - - -
309T GLU* 1.3 77.7 - - - +
311T LEU* 1.3 60.2 - - - +
313T ARG* 3.7 5.4 + - - +
314T HIS* 2.8 35.2 + - + -
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Residues in contact with LEU 311 (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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268C ARG* 3.8 24.9 - - - +
306C ASP 4.7 0.2 - - - +
307C TYR* 4.0 26.9 - - + -
308C PHE* 4.3 24.2 - - + -
65T GLU* 3.6 33.0 - - + +
66T ILE* 4.3 7.2 - - + -
237T PHE* 3.9 24.7 - - + -
307T LEU 3.2 11.2 + - - +
308T LEU* 3.0 7.9 + - + +
310T GLN* 1.3 78.5 - - - +
312T MET* 1.3 62.4 + - + +
314T HIS* 3.1 13.3 + - - +
315T TYR* 3.4 23.1 - - + -
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Residues in contact with MET 312 (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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308C PHE* 4.1 12.1 - - - -
69T GLY* 3.8 25.8 - - - +
72T ALA* 3.7 26.7 - - + -
281T MET* 3.4 44.2 + - + +
282T MET* 3.6 25.1 - - + +
285T TYR* 4.1 15.7 - - + -
308T LEU* 2.8 43.0 + - + +
311T LEU* 1.3 67.9 - - + +
313T ARG* 1.3 61.8 + - - +
314T HIS 3.0 6.6 + - - -
315T TYR* 3.2 19.8 + - - +
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Residues in contact with ARG 313 (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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231T VAL* 3.5 4.1 - - - +
232T ASN* 2.6 37.1 + - - +
280T ASP* 3.0 39.9 + - - +
282T MET* 4.0 15.8 - - + +
283T GLU* 3.8 15.8 - - - +
286T ASN* 4.7 8.1 - - - +
309T GLU* 3.1 52.9 + - + +
310T GLN* 4.1 6.3 - - - +
311T LEU 3.3 0.4 - - - -
312T MET* 1.3 75.8 - - - +
314T HIS* 1.3 60.0 + - + +
315T TYR 3.4 1.6 - - - -
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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