Contacts of the helix formed by residues 362 - 366 (chain A) in PDB entry 3LPK
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 LEU 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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343A VAL* 3.7 24.9 - - + -
360A THR* 5.2 1.8 - - + -
361A ILE* 1.3 76.8 - - - +
363A PRO* 1.3 68.7 - - + +
364A GLN* 2.9 17.5 - - + +
365A GLN* 2.8 32.9 + - - +
366A TYR* 3.2 15.7 + - - -
422A VAL 3.9 4.5 - - - +
423A HIS* 3.6 37.7 - - + -
424A ASP* 4.8 0.4 - - - +
427A ARG* 3.7 25.4 - - + +
428A THR 3.6 23.8 - - - +
429A ALA* 3.9 7.9 - - - +
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Residues in contact with PRO 363 (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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338A TRP* 3.7 26.0 - - + +
341A PHE* 3.6 23.6 - - + -
342A PRO 3.9 13.5 - - - +
362A LEU* 1.3 88.9 - - + +
364A GLN* 1.3 65.1 + - - +
365A GLN 2.9 0.4 - - - -
366A TYR* 3.5 20.0 - - + -
367A LEU* 2.8 37.9 + - + +
427A ARG* 3.5 31.0 - - - +
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Residues in contact with GLN 364 (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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219A GLY* 5.8 1.9 - - - -
338A TRP* 3.4 44.6 - - + +
362A LEU* 2.9 17.1 - - + +
363A PRO* 1.3 88.4 - - - +
365A GLN* 1.3 61.1 + - - +
367A LEU 3.8 9.2 - - - +
369A PRO* 5.4 4.3 - - - +
400A GLU* 5.6 1.2 - - - +
422A VAL* 3.5 47.4 - - + +
423A HIS* 3.7 8.4 + - - +
424A ASP* 2.9 43.3 + - - +
427A ARG* 5.0 0.7 + - - -
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Residues in contact with GLN 365 (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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361A ILE* 3.8 21.2 - - + -
362A LEU* 2.8 42.0 + - - +
364A GLN* 1.3 82.7 + - - +
366A TYR* 1.3 62.5 + - - +
367A LEU 3.3 4.7 + - - +
368A ARG* 5.1 0.7 - - - -
397A VAL* 3.3 45.6 - - - +
400A GLU* 4.7 9.3 + - + +
401A GLY* 4.0 22.9 - - - +
421A HIS* 4.1 9.0 - - - +
422A VAL* 3.0 39.4 + - - +
429A ALA* 4.2 4.3 - - - +
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Residues in contact with TYR 366 (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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309A ILE* 4.4 5.5 - - + +
341A PHE* 3.5 13.4 - + - +
342A PRO* 2.6 49.8 + - - +
344A ILE* 3.7 26.9 - - + -
361A ILE* 3.9 15.9 - - + -
362A LEU 3.2 16.9 + - - -
363A PRO* 3.5 21.8 - - + -
365A GLN* 1.3 78.0 - - - +
367A LEU* 1.3 74.5 + - + +
368A ARG 3.9 0.9 - - - -
383A PHE* 4.0 20.4 - + - -
384A ALA* 2.8 33.3 + - - +
385A ILE* 3.9 22.0 - - + -
397A VAL* 4.8 4.3 - - + -
398A ILE* 5.3 0.9 - - + -
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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