Contacts of the helix formed by residues 364 - 371 (chain D) in PDB entry 1R4N
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 VAL 364 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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355D PHE* 5.3 12.1 - - + +
360D LYS 4.1 3.4 - - - +
361D LEU* 2.8 49.1 - - + +
363D GLU* 1.3 76.5 - - - +
365D LEU* 1.3 63.8 + - - +
366D ASP 3.6 0.2 - - - -
367D TYR* 3.8 11.9 - - + +
368D LEU* 3.1 32.7 + - + +
381D ILE* 4.2 17.9 - - + -
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Residues in contact with LEU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D LEU 3.9 6.0 + - - +
362D GLN* 3.7 7.9 + - - +
364D VAL* 1.3 79.3 - - - +
366D ASP* 1.3 63.2 + - - +
367D TYR 3.0 2.1 + - - -
368D LEU* 3.0 5.0 + - + +
369D THR* 2.7 44.1 + - - +
379D PRO* 4.5 20.6 - - + +
380D ALA* 5.7 1.1 - - - -
381D ILE* 4.8 17.0 - - + +
393D TYR* 3.0 37.9 - - + +
395D GLN* 4.1 24.0 - - - +
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Residues in contact with ASP 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D GLN* 2.8 26.0 + - - +
363D GLU* 5.1 3.4 - - - -
365D LEU* 1.3 86.1 - - - +
367D TYR* 1.3 57.3 + - - +
369D THR* 4.4 4.4 - - - +
370D ASN* 3.0 49.1 + - - +
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Residues in contact with TYR 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351D GLN* 5.6 4.6 + - + +
353D ILE* 3.9 20.9 - - + +
355D PHE* 4.2 44.8 - + + -
363D GLU 3.7 21.2 + - - +
364D VAL* 3.8 10.6 - - + +
365D LEU 3.0 1.0 - - - -
366D ASP* 1.3 75.5 - - - +
368D LEU* 1.3 72.3 + - + +
371D SER* 2.8 61.1 + - - +
373D SER* 4.7 4.7 + - - -
374D LEU* 3.9 20.2 - - + +
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Residues in contact with LEU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D VAL* 3.1 22.2 - - + +
365D LEU* 3.0 6.8 + - + +
367D TYR* 1.3 90.5 - - + +
369D THR* 1.3 61.7 + - - +
371D SER 4.4 0.2 + - - -
374D LEU* 3.3 35.8 - - + +
375D GLN 3.6 1.2 + - - -
376D MET* 3.3 34.8 + - - +
379D PRO* 4.5 15.9 - - + -
381D ILE* 4.3 19.5 - - + -
904D VAL* 4.1 25.8 - - + -
916D PHE* 5.7 10.1 - - + -
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Residues in contact with THR 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D LEU* 2.7 33.0 + - - +
366D ASP* 4.3 6.3 - - - +
368D LEU* 1.3 75.4 - - - +
370D ASN* 1.3 70.4 + - - +
375D GLN* 3.9 8.1 - - - -
376D MET 3.6 22.2 - - - +
377D LYS* 5.5 0.7 - - - -
378D SER 5.3 2.9 - - - +
379D PRO* 3.6 22.0 - - + +
395D GLN* 5.5 0.2 + - - -
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Residues in contact with ASN 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D ASP* 3.0 41.6 + - - +
369D THR* 1.3 92.3 - - - +
371D SER* 1.3 68.9 + - - +
372D ALA* 2.8 7.6 + - - +
375D GLN* 4.9 3.4 - - - +
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Residues in contact with SER 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366D ASP 4.1 0.4 + - - -
367D TYR* 2.8 53.6 + - - +
370D ASN* 1.3 68.6 - - - +
372D ALA* 1.3 54.4 + - - +
373D SER* 2.4 37.0 + - - -
374D LEU* 2.8 21.4 + - - -
375D GLN 3.1 9.2 + - - -
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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