Contacts of the helix formed by residues 396 - 407 (chain A) in PDB entry 5CXV
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 PRO 396 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A ASP 5.5 0.7 - - - +
394A CYS 3.6 8.1 - - - +
395A VAL* 1.3 93.4 - - + +
397A GLU* 1.3 65.8 + - - +
398A THR* 4.3 9.6 - - - +
399A LEU* 3.0 28.6 + - + +
400A TRP* 2.9 21.2 + - - -
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Residues in contact with GLU 397 (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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396A PRO* 1.3 73.6 - - - +
398A THR* 1.3 63.0 + - - +
400A TRP* 3.1 13.7 + - - +
401A GLU* 2.9 39.4 + - + +
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Residues in contact with THR 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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20A LYS* 5.9 2.0 - - - +
396A PRO* 3.2 8.6 - - - +
397A GLU* 1.3 77.8 - - - +
399A LEU* 1.3 55.6 + - - +
401A GLU* 3.3 17.0 + - - +
402A LEU* 3.0 29.2 + - + +
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Residues in contact with LEU 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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384A MET* 3.3 23.1 - - + +
395A VAL* 3.6 22.7 - - + -
396A PRO* 3.0 31.0 + - + +
398A THR* 1.3 76.7 - - - +
400A TRP* 1.3 65.1 + - - +
402A LEU* 3.3 17.0 + - + +
403A GLY* 2.9 20.6 + - - +
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Residues in contact with TRP 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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189A THR* 6.5 0.7 - - + -
381A TYR* 3.8 31.6 - + - -
384A MET* 3.5 43.2 - - + +
385A VAL* 3.8 20.4 - - + -
388A SER* 3.7 17.5 - - - -
393A ASP* 6.3 0.2 - - - +
395A VAL* 3.2 38.4 + - + +
396A PRO 2.9 27.4 + - - -
397A GLU* 3.1 11.0 + - - +
399A LEU* 1.3 75.7 - - - +
401A GLU* 1.3 63.2 + - + +
403A GLY* 3.9 0.2 - - - -
404A TYR* 2.9 27.1 + - - +
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Residues in contact with GLU 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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20A LYS* 3.2 27.2 + - - -
82A TYR* 3.2 17.0 + - - +
86A LEU* 3.7 26.3 - - + +
397A GLU* 2.9 31.5 + - + +
398A THR* 3.6 15.8 + - - +
400A TRP* 1.3 77.0 - - + +
402A LEU* 1.3 57.1 + - - +
405A TRP* 2.9 29.2 + - - +
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Residues in contact with LEU 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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398A THR* 3.0 17.4 + - + +
399A LEU* 3.9 15.7 - - + +
401A GLU* 1.3 77.3 - - - +
403A GLY* 1.3 58.6 + - - +
405A TRP* 3.2 20.7 + - + +
406A LEU* 2.9 34.1 + - + +
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Residues in contact with GLY 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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377A THR 4.7 0.5 - - - +
380A PRO* 5.1 5.6 - - - -
381A TYR* 3.7 15.7 + - - +
384A MET* 4.4 14.6 - - - -
399A LEU* 2.9 17.3 + - - +
400A TRP 3.9 0.4 - - - -
402A LEU* 1.3 74.8 - - - +
404A TYR* 1.3 64.6 + - - +
406A LEU* 3.5 12.6 + - - +
407A CYS* 3.4 19.9 + - - -
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Residues in contact with TYR 404 (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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82A TYR* 3.4 44.4 - + - +
101A TRP* 4.6 4.4 - + - -
102A LEU* 4.4 10.7 - - + +
105A ASP* 3.4 13.5 + - - -
106A TYR* 3.6 26.9 - - - -
381A TYR* 3.5 30.5 - + + -
400A TRP 2.9 17.7 + - - +
403A GLY* 1.3 76.4 - - - +
405A TRP* 1.3 60.6 + - - +
406A LEU 3.3 0.5 + - - -
407A CYS* 3.4 9.1 + - - +
408A TYR* 3.3 24.2 + - - -
501A 0HK 3.4 41.8 - - + -
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Residues in contact with TRP 405 (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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28A ILE* 6.0 2.0 - - + -
31A THR* 5.6 2.5 - - - -
32A THR* 3.2 42.3 - - + +
35A LEU* 4.4 23.2 - - + +
79A MET* 5.5 1.8 - - - +
82A TYR* 4.0 17.7 - + + -
83A THR* 3.9 17.1 + - + -
86A LEU* 5.7 2.2 - - + -
401A GLU 2.9 18.6 + - - +
402A LEU* 3.2 21.7 + - + +
404A TYR* 1.3 77.3 - - - +
406A LEU* 1.3 73.1 + - + +
408A TYR* 3.3 34.1 + + - +
409A VAL* 4.2 21.1 - - + +
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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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376A LEU 4.0 2.2 - - - +
377A THR* 3.5 38.6 - - + +
380A PRO* 3.9 26.9 - - + -
402A LEU* 2.9 21.7 + - + +
403A GLY* 3.9 7.0 - - - +
404A TYR 3.2 0.8 - - - -
405A TRP* 1.3 86.1 - - + +
407A CYS* 1.3 65.1 + - - +
408A TYR 3.0 3.9 + - - -
409A VAL* 3.1 28.6 + - + +
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Residues in contact with CYS 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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377A THR 3.6 15.7 - - - -
378A TRP* 2.8 46.3 + - + +
381A TYR* 3.9 17.3 - - - -
403A GLY 3.4 17.7 - - - -
404A TYR 4.1 2.0 - - - -
405A TRP 3.3 1.0 - - - -
406A LEU* 1.3 75.9 - - - +
408A TYR* 1.3 58.3 + - - +
409A VAL 3.3 0.2 - - - -
410A ASN* 2.8 12.2 - - - +
411A SER* 5.0 0.3 + - - -
501A 0HK 3.7 43.3 - - + -
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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