Contacts of the helix formed by residues 330 - 342 (chain T) in PDB entry 2P8Z
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 ALA 330 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35T LEU* 5.5 3.4 - - + -
38T SER* 4.0 10.5 - - - +
213T SER 4.9 5.2 - - - +
214T GLY* 5.5 4.9 - - - +
217T GLY* 2.4 45.8 + - - +
218T TRP* 2.9 35.8 - - - +
219T ALA* 3.4 6.3 - - + +
329T PRO 2.7 21.6 - - - -
331T ALA* 1.3 69.5 + - - +
332T ASP 3.0 1.6 - - - -
333T ALA* 2.7 19.6 + - - +
334T LEU* 3.2 17.1 + - + +
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Residues in contact with ALA 331 (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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38T SER* 3.7 17.3 + - - +
39T LEU* 4.3 12.8 - - + -
42T ARG* 3.2 42.6 - - + -
329T PRO* 4.2 1.5 - - + -
330T ALA* 1.3 77.2 - - - +
332T ASP* 1.3 57.3 + - - +
334T LEU* 3.2 4.4 + - - +
335T LEU* 2.8 40.4 + - + +
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Residues in contact with ASP 332 (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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42T ARG* 2.9 40.7 + - - -
81T MET* 5.9 0.3 - - - +
224T GLN* 4.4 15.5 + - - +
329T PRO* 2.4 53.3 + - + +
330T ALA 2.9 0.8 + - - -
331T ALA* 1.3 77.4 - - - +
333T ALA* 1.3 59.5 + - - +
335T LEU* 4.1 6.3 - - - +
336T GLU* 3.1 24.6 + - - +
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Residues in contact with ALA 333 (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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210T ALA* 4.6 7.2 - - + -
219T ALA* 2.8 49.4 - - + -
220T PHE* 3.3 12.3 - - - +
221T THR* 4.2 6.5 - - - +
224T GLN* 4.8 4.7 - - - +
329T PRO 3.7 1.6 + - - -
330T ALA 2.7 8.3 + - - -
332T ASP* 1.3 75.8 - - - +
334T LEU* 1.3 61.7 + - - +
336T GLU* 3.3 7.2 + - - +
337T MET* 3.3 25.5 + - - +
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Residues in contact with LEU 334 (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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35T LEU* 4.2 27.4 - - + +
38T SER* 5.2 2.2 - - - +
39T LEU* 4.0 28.5 - - + -
126T LEU* 4.4 14.6 - - + -
156T VAL* 3.3 41.7 - - + -
210T ALA* 4.4 4.7 - - + -
219T ALA* 5.3 3.6 - - + -
330T ALA* 3.7 14.8 - - + +
331T ALA* 3.2 8.4 + - - +
333T ALA* 1.3 75.8 - - + +
335T LEU* 1.3 65.1 + - - +
337T MET* 3.1 13.0 + - + +
338T ILE* 3.0 32.1 + - + +
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Residues in contact with LEU 335 (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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35S THR* 4.0 27.8 - - + -
39T LEU* 3.8 18.4 - - + -
42T ARG* 4.2 18.4 - - + +
43T ALA* 4.2 0.9 - - + -
77T LEU* 4.3 4.7 - - + -
79T SER* 4.3 20.2 - - - +
81T MET* 4.7 4.9 - - + -
100T ILE* 3.8 25.8 - - + -
331T ALA* 2.8 32.4 + - + +
332T ASP* 4.1 9.2 - - - +
334T LEU* 1.3 73.5 - - - +
336T GLU* 1.3 57.6 + - - +
338T ILE* 3.6 6.0 - - + +
339T VAL* 2.9 36.7 + - - +
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Residues in contact with GLU 336 (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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81T MET* 4.7 16.1 - - + +
85T ASP* 5.5 4.9 - - - +
207T GLY* 5.1 2.1 - - - +
221T THR* 2.3 42.7 + - - +
223T ARG* 4.4 14.0 + - - +
224T GLN* 3.0 32.5 + - - +
332T ASP 3.1 19.6 + - - +
333T ALA 3.4 4.9 - - - +
334T LEU 3.1 0.6 - - - -
335T LEU* 1.3 76.5 - - - +
337T MET* 1.3 58.6 + - - +
340T LEU* 3.0 55.8 + - + +
341T HIS* 5.2 0.4 - - + -
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Residues in contact with MET 337 (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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126T LEU* 4.1 3.1 - - + -
154T VAL* 3.3 30.9 - - + +
155T VAL 3.5 13.0 - - - +
156T VAL* 3.8 11.9 - - + -
207T GLY 3.2 16.6 - - - +
208T THR 3.6 5.6 - - - -
209T VAL 3.6 17.0 - - - -
210T ALA* 3.5 37.5 - - + -
221T THR* 4.5 8.1 - - + -
333T ALA 3.3 7.8 + - - +
334T LEU* 3.1 14.8 + - + +
336T GLU* 1.3 76.9 - - - +
338T ILE* 1.3 59.2 + - - +
341T HIS* 2.9 38.9 + - - +
342T LEU* 3.4 4.6 + - - +
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Residues in contact with ILE 338 (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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20T ARG* 3.4 18.7 + - + -
22T MET* 3.8 23.3 - - + -
39T LEU* 4.4 18.2 - - + -
100T ILE* 3.8 34.3 - - + -
126T LEU* 5.1 8.3 - - + -
154T VAL* 5.7 2.0 - - + -
334T LEU* 3.0 26.9 + - + +
335T LEU* 3.3 15.9 + - + +
337T MET* 1.3 78.1 - - + +
339T VAL* 1.3 62.0 + - - +
342T LEU* 3.2 50.0 + - + +
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Residues in contact with VAL 339 (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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20T ARG* 2.7 34.8 + - + +
79T SER* 4.3 3.4 - - - +
81T MET* 3.6 42.0 - - + -
89T ILE* 3.9 11.1 - - + +
98T PHE* 3.7 45.5 - - + -
100T ILE* 4.2 16.4 - - + -
335T LEU 2.9 22.1 + - - +
336T GLU 4.3 0.2 - - - +
338T ILE* 1.3 73.8 - - - +
340T LEU* 1.3 61.5 + - + +
342T LEU 4.2 0.5 - - - +
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Residues in contact with LEU 340 (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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81T MET* 5.1 4.5 - - - -
85T ASP* 3.6 25.1 - - + +
88T GLU* 4.6 8.3 - - + +
89T ILE* 3.2 48.5 - - + +
90T LYS* 4.7 3.8 + - - +
91T GLN* 4.6 3.2 + - - -
223T ARG* 4.2 27.1 - - - +
336T GLU* 3.0 39.1 + - + +
339T VAL* 1.3 82.7 - - + +
341T HIS* 1.3 81.9 + - + +
342T LEU 4.9 0.2 - - - -
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Residues in contact with HIS 341 (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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91T GLN* 4.7 3.5 + - - -
152T LYS* 2.9 33.6 + - - +
154T VAL* 4.1 7.9 - - + -
206T ARG* 3.2 29.2 + - + -
207T GLY* 3.5 22.4 + - - -
208T THR* 3.5 24.4 - - + +
336T GLU* 4.6 0.7 - - + -
337T MET* 2.9 25.2 + - - +
340T LEU* 1.3 102.1 + - + +
342T LEU* 1.3 65.3 + - - +
343T PRO* 3.5 0.9 - - - +
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Residues in contact with LEU 342 (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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20T ARG* 3.0 28.4 + - + -
21T ASN 6.0 0.2 - - - +
22T MET* 3.9 31.2 - - + -
91T GLN* 3.3 6.8 + - - -
124T GLY* 4.0 4.3 - - - -
125T ALA 3.9 12.8 - - - +
126T LEU 4.9 0.2 - - - +
152T LYS* 3.5 29.2 - - + +
153T PRO 4.6 0.2 - - - -
154T VAL* 4.0 27.6 - - + -
337T MET 4.1 1.3 - - - +
338T ILE* 3.2 43.6 + - + +
339T VAL 4.2 0.5 - - - +
341T HIS* 1.3 78.1 - - - +
343T PRO* 1.3 69.6 - - + +
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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