Contacts of the helix formed by residues 397 - 407 (chain A) in PDB entry 3C51
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 GLU 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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396A VAL* 1.3 89.0 - - - +
398A ASN* 1.3 61.4 + - - +
399A LYS* 4.2 6.0 - - + +
400A GLU* 3.7 36.1 + - + +
401A LEU* 3.0 29.5 + - - +
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Residues in contact with ASN 398 (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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349A TYR* 3.4 23.8 + - - -
353A PRO* 4.2 28.0 - - - +
356A MET* 4.9 3.0 - - - +
361A LEU* 4.9 7.0 - - + +
396A VAL 4.8 3.3 - - - +
397A GLU* 1.3 74.7 - - - +
399A LYS* 1.3 58.2 + - + +
401A LEU* 4.2 4.8 - - - +
402A LYS* 3.0 30.2 + - - +
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Residues in contact with LYS 399 (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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397A GLU* 3.4 7.2 - - + +
398A ASN* 1.3 77.5 - - + +
400A GLU* 1.3 61.6 + - - +
402A LYS* 3.7 19.7 - - + +
403A GLN* 3.4 24.3 + - - +
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Residues in contact with GLU 400 (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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396A VAL* 4.7 10.8 - - + -
397A GLU* 3.3 43.7 + - + +
398A ASN 3.3 0.4 - - - -
399A LYS* 1.3 76.8 - - - +
401A LEU* 1.3 66.0 + - - +
403A GLN* 3.3 12.1 + - - +
404A ARG* 3.0 47.8 + - - +
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Residues in contact with LEU 401 (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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353A PRO* 4.0 11.2 - - + +
354A GLY* 3.4 39.3 - - - +
389A PHE* 5.1 6.5 - - + -
390A ARG* 4.4 26.5 - - + +
396A VAL* 4.4 17.4 - - + +
397A GLU 3.0 16.3 + - - +
398A ASN* 4.2 5.2 - - - +
400A GLU* 1.3 76.9 - - - +
402A LYS* 1.3 52.1 + - - +
404A ARG* 3.0 26.8 + - + +
405A VAL* 2.7 42.7 + - + +
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Residues in contact with LYS 402 (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 LEU* 4.0 44.1 + - + +
362A LEU* 4.2 13.2 - - - +
398A ASN 3.0 20.8 + - - +
399A LYS* 3.7 20.2 - - + +
401A LEU* 1.3 75.9 - - - +
403A GLN* 1.3 56.7 + - + +
405A VAL* 2.9 2.8 + - - +
406A LEU* 2.6 66.5 + - + +
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Residues in contact with GLN 403 (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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399A LYS 3.4 12.7 + - - +
400A GLU* 3.3 16.2 + - - +
402A LYS* 1.3 82.1 - - + +
404A ARG* 1.3 57.6 + - + +
406A LEU* 4.5 4.9 - - - +
407A GLU* 2.8 56.8 + - - +
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Residues in contact with ARG 404 (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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389A PHE* 3.3 30.7 + - + -
390A ARG* 5.5 2.4 - - - +
394A GLU* 4.0 28.0 + - - -
396A VAL* 5.1 9.0 - - - +
400A GLU* 3.0 37.2 + - - +
401A LEU* 3.0 35.1 + - + +
403A GLN* 1.3 75.2 - - + +
405A VAL* 1.3 58.6 + - - +
407A GLU 4.4 0.7 - - - -
408A GLN* 2.9 51.6 + - - +
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Residues in contact with VAL 405 (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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354A GLY* 5.3 7.6 - - - -
356A MET 4.0 8.5 - - - +
358A PRO* 3.7 24.2 - - + -
361A LEU* 4.0 14.1 - - + -
373A PHE* 3.7 29.6 - - + -
389A PHE* 4.0 21.8 - - + -
401A LEU* 2.7 30.6 + - + +
402A LYS 2.9 5.3 + - - +
404A ARG* 1.3 75.5 - - - +
406A LEU* 1.3 66.6 + - - +
407A GLU 3.0 2.9 + - - -
408A GLN 3.8 1.0 + - - -
430A LYS* 3.3 25.3 + - - +
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Residues in contact with LEU 406 (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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358A PRO* 3.4 33.7 - - + +
361A LEU* 4.7 2.0 - - + -
362A LEU* 3.4 42.0 - - + -
402A LYS* 2.6 55.5 + - + +
403A GLN* 4.6 5.2 - - - +
405A VAL* 1.3 74.0 - - - +
407A GLU* 1.3 73.4 + - + +
430A LYS* 4.5 15.0 - - + +
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Residues in contact with GLU 407 (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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403A GLN* 2.8 41.8 + - - +
404A ARG* 4.4 0.5 - - - -
405A VAL 3.0 0.2 + - - -
406A LEU* 1.3 84.5 - - + +
408A GLN* 1.3 61.7 + - - +
430A LYS* 5.6 0.2 - - - +
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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