Contacts of the helix formed by residues 378 - 387 (chain A) in PDB entry 2P02
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 ARG 378 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A GLU* 3.6 37.5 + - - +
151A ASP* 3.0 25.7 + - - -
347A SER* 3.6 26.7 - - - +
348A HIS* 3.5 38.3 + - - +
349A PRO* 4.3 0.8 - - - +
376A ASP* 2.8 37.1 + - - +
377A LEU* 1.3 79.2 - - - +
379A PRO* 1.4 71.1 - - + +
381A VAL* 3.0 21.3 + - + +
382A ILE* 2.9 20.4 + - - +
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Residues in contact with PRO 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 3.9 22.9 - - + +
153A GLY 4.1 2.9 - - - +
154A ALA* 4.0 21.1 - - - +
309A TYR* 3.8 19.5 - - - +
310A THR 5.0 2.0 - - - +
312A VAL* 4.0 17.0 - - + -
315A SER* 4.5 2.5 + - - +
342A TYR* 4.2 7.6 - - + -
347A SER 3.3 18.4 - - - +
377A LEU 3.5 4.5 - - - +
378A ARG* 1.4 83.7 - - + +
380A GLY* 1.3 56.9 + - - +
382A ILE* 3.8 11.5 - - + +
383A VAL* 3.0 30.7 + - - +
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Residues in contact with GLY 380 (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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149A GLU* 3.3 27.9 - - - +
150A GLU* 3.6 24.0 + - - +
152A ILE* 3.9 10.0 + - - +
309A TYR* 4.5 0.4 - - - -
378A ARG 3.2 1.0 - - - -
379A PRO* 1.3 79.6 - - - +
381A VAL* 1.3 62.2 + - - +
383A VAL* 3.5 19.1 - - - +
384A ARG* 4.7 4.3 + - - +
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A GLU* 4.0 17.5 - - + +
376A ASP* 3.7 28.9 - - + +
378A ARG* 3.0 44.6 + - + +
380A GLY* 1.3 80.0 - - - +
382A ILE* 1.3 66.9 + - - +
383A VAL 3.1 1.1 - - - -
384A ARG* 3.0 35.3 + - - +
385A ASP* 3.0 26.7 + - - +
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Residues in contact with ILE 382 (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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312A VAL* 5.9 0.2 - - + -
315A SER* 3.6 25.8 - - - +
316A ALA* 4.2 5.4 - - + +
319A ALA* 3.7 23.1 - - + -
322A TRP* 6.1 2.0 - - + -
342A TYR* 4.1 9.0 - - + +
376A ASP 4.0 2.9 - - - +
377A LEU* 3.4 35.2 - - + +
378A ARG 2.9 17.2 + - - +
379A PRO* 3.8 9.2 - - + +
381A VAL* 1.3 77.3 - - - +
383A VAL* 1.3 63.2 + - - +
385A ASP* 4.5 6.5 - - - +
386A LEU* 2.8 44.7 + - + +
388A LEU* 3.8 10.5 - - + -
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A GLU* 3.8 16.4 - - - +
309A TYR* 3.4 48.5 - - + -
379A PRO 3.0 12.2 + - - +
380A GLY* 3.5 22.0 - - - +
382A ILE* 1.3 76.2 - - - +
384A ARG* 1.3 61.3 + - + +
387A ASP* 3.0 23.0 + - - -
388A LEU* 3.0 25.0 + - + +
389A LYS* 3.8 24.5 - - + -
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Residues in contact with ARG 384 (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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149A GLU* 5.8 1.3 - - - +
150A GLU* 2.9 37.0 + - - +
380A GLY 4.7 4.9 + - - +
381A VAL* 3.0 32.5 + - - +
383A VAL* 1.3 82.9 - - + +
385A ASP* 1.3 75.2 + - - +
386A LEU 3.3 0.7 + - - -
387A ASP* 3.5 9.9 + - - +
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Residues in contact with ASP 385 (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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322A TRP* 3.8 37.3 - - + -
376A ASP* 4.7 6.6 + - - +
381A VAL* 3.0 33.8 + - - +
382A ILE* 3.9 5.2 + - - +
384A ARG* 1.3 87.7 + - - +
386A LEU* 1.3 65.9 + - + +
387A ASP* 3.9 0.5 + - - +
408A PRO* 4.4 5.0 - - - +
413A LYS* 5.2 5.1 + - - -
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Residues in contact with LEU 386 (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 TYR* 4.0 15.3 - - + -
319A ALA* 3.8 26.7 - - + +
322A TRP* 3.8 28.7 - - + -
382A ILE* 2.8 34.8 + - + +
385A ASP* 1.3 83.8 - - + +
387A ASP* 1.3 70.4 + - - +
388A LEU* 3.4 21.8 + - + +
408A PRO* 3.5 26.4 - - + +
409A TRP* 3.8 28.7 - - + +
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Residues in contact with ASP 387 (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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383A VAL 3.0 10.4 + - - -
384A ARG 3.5 8.9 + - - +
385A ASP 3.5 1.3 - - - +
386A LEU* 1.3 79.7 - - - +
388A LEU* 1.3 57.6 + - - +
389A LYS* 3.3 6.4 + - - +
390A LYS* 2.8 67.5 + - + +
392A ILE* 5.7 1.4 - - - +
408A PRO* 4.6 8.7 - - + -
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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