Contacts of the helix formed by residues 380 - 387 (chain A) in PDB entry 4P3N
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 SER 380 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A PHE 3.8 0.2 + - - -
379A ASN* 1.3 75.0 + - - +
381A ARG* 1.3 62.4 + - - +
383A TRP* 3.2 13.3 + - - +
384A MET* 3.0 21.7 + - - +
389A TRP* 3.3 32.3 + - - -
405A LEU* 2.7 40.2 + - - +
406A PHE* 5.2 0.2 - - - +
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Residues in contact with ARG 381 (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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379A ASN* 3.0 20.8 + - - +
380A SER* 1.3 78.7 - - - +
382A LEU* 1.3 55.7 + - - +
384A MET* 3.2 8.6 + - - +
385A THR* 2.9 33.3 + - - +
404A GLU* 2.6 38.6 + - - -
337B GLU* 2.8 39.0 + - - -
338B LEU* 3.7 19.6 - - + +
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Residues in contact with LEU 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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378A PHE* 3.4 44.2 - - + -
379A ASN 3.2 11.2 + - - +
381A ARG* 1.3 78.1 - - - +
383A TRP* 1.3 65.7 + - + +
385A THR* 2.9 8.2 + - - +
386A SER* 2.9 26.3 + - - -
414A PRO* 3.7 22.0 - - + -
415A GLY 4.7 0.9 - - - +
418A LEU* 3.6 25.8 - - + -
571A PHE* 3.5 28.5 - - + -
338B LEU* 3.7 24.5 - - + +
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Residues in contact with TRP 383 (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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378A PHE* 3.4 51.0 + + + +
379A ASN 3.2 20.4 - - - -
380A SER* 3.2 6.8 + - - +
382A LEU* 1.3 78.6 - - + +
384A MET* 1.3 57.7 + - - +
386A SER* 3.5 7.9 - - - -
387A GLY 3.0 5.7 + - - -
388A HIS* 3.0 64.6 + + + -
389A TRP* 3.0 26.9 + + + -
396A MET* 3.8 10.8 - - + -
407A ALA* 3.6 23.0 + - + +
409A LYS* 3.5 38.6 - - + -
410A PRO* 3.8 10.1 - - + -
411A MET 4.0 4.7 - - - -
414A PRO* 3.8 20.2 - - + -
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Residues in contact with MET 384 (chain A).
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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380A SER* 3.0 17.3 + - - +
381A ARG* 3.5 9.4 - - - +
382A LEU 3.1 0.2 - - - -
383A TRP* 1.3 77.3 - - - +
385A THR* 1.3 62.0 + - - +
389A TRP* 3.8 23.1 - - + -
390A GLN* 2.8 49.6 - - - +
570A ARG* 4.0 9.2 + - - -
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Residues in contact with THR 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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381A ARG 2.9 16.1 + - - -
382A LEU* 2.9 12.2 + - - -
384A MET* 1.3 80.3 - - - +
386A SER* 1.3 59.9 + - - +
570A ARG* 3.0 57.9 + - - +
571A PHE* 3.8 28.0 - - + -
338B LEU* 6.1 0.3 - - - +
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Residues in contact with SER 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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382A LEU 2.9 8.5 + - - -
383A TRP* 3.3 14.4 + - - -
385A THR* 1.3 77.6 - - - +
387A GLY* 1.3 59.5 + - - +
388A HIS* 2.6 35.9 + - - -
414A PRO* 3.6 25.4 - - - -
567A LEU* 4.3 18.7 - - - +
570A ARG* 4.6 7.0 - - - +
571A PHE* 4.2 9.2 - - - -
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Residues in contact with GLY 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 TRP 3.0 4.4 + - - -
385A THR 3.3 3.2 - - - -
386A SER* 1.3 80.0 - - - +
388A HIS* 1.3 65.0 + - - +
389A TRP 3.2 2.5 - - - -
390A GLN* 3.1 24.0 + - - +
391A HIS* 2.9 38.7 + - - +
570A ARG* 5.0 4.5 - - - -
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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