Contacts of the helix formed by residues 395 - 404 (chain A) in PDB entry 6BHG
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 395 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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346A VAL* 4.3 4.9 - - + -
348A LEU* 4.2 9.6 - - + -
354A ILE* 3.9 23.3 - - + -
355A LYS 4.2 2.5 - - - -
356A THR* 4.0 8.1 - - + +
375A VAL* 4.0 11.9 - - + -
377A ILE* 4.0 24.7 - - + -
388A ILE* 4.1 15.3 - - + -
389A TYR 3.4 22.4 - - - +
390A ARG* 3.8 19.7 - - - +
392A SER 3.1 10.4 + - - +
393A THR 3.8 1.2 - - - +
394A ARG* 1.3 76.0 - - - +
396A GLU* 1.3 67.8 + - - +
397A PRO* 3.3 5.2 - - + -
398A MET* 3.0 18.1 + - + +
399A PHE 3.0 9.4 + - - -
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Residues in contact with GLU 396 (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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355A LYS* 2.9 33.7 + - + +
362A TRP* 3.9 14.1 - - + -
394A ARG 3.7 1.4 + - - -
395A LEU* 1.3 69.7 - - - +
397A PRO* 1.3 78.6 - - + +
399A PHE* 3.1 6.2 + - + +
400A SER* 2.8 45.3 + - - -
518A UNX 2.7 31.5 - - - -
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Residues in contact with PRO 397 (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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346A VAL* 3.8 22.0 - - + +
348A LEU* 4.5 11.4 - - + -
352A GLN* 5.3 3.1 - - - +
354A ILE* 4.1 31.2 - - + -
395A LEU* 3.4 6.3 - - + -
396A GLU* 1.3 106.0 - - + +
398A MET* 1.3 55.1 - - - +
400A SER* 3.8 2.8 - - - -
401A MET* 3.1 28.4 + - - +
534A UNX 3.8 19.3 - - - -
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Residues in contact with MET 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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344A PRO* 3.8 35.4 - - + +
345A MET* 3.9 3.1 - - - -
346A VAL* 3.6 31.4 - - + +
390A ARG 3.5 17.5 - - - +
391A GLY* 3.9 14.8 - - - +
392A SER 3.2 27.1 - - - +
393A THR* 3.9 4.0 - - + -
395A LEU* 3.0 4.5 + - + +
397A PRO* 1.3 75.8 - - - +
399A PHE* 1.3 67.5 + - - +
401A MET* 3.4 12.7 + - - +
402A LYS* 3.0 47.6 + - + +
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Residues in contact with PHE 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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362A TRP* 3.7 32.5 - + + -
393A THR* 3.3 37.3 - - + +
395A LEU 3.0 6.3 + - - +
396A GLU* 3.5 11.0 - - + +
398A MET* 1.3 77.7 - - - +
400A SER* 1.3 53.1 + - - +
402A LYS* 3.3 1.9 + - - +
403A THR* 2.7 67.7 + - + +
16B PRO* 4.3 11.0 - - + -
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Residues in contact with SER 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 GLU* 2.8 33.6 + - - -
397A PRO* 3.8 5.4 - - - -
399A PHE* 1.3 77.6 - - - +
401A MET* 1.3 66.6 + - - +
403A THR* 2.8 18.1 + - - -
404A SER* 3.1 19.2 + - - -
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Residues in contact with MET 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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344A PRO* 5.1 10.1 - - - -
345A MET 5.2 5.2 - - - +
346A VAL* 4.3 21.5 - - + -
397A PRO 3.1 13.7 + - - +
398A MET* 3.8 18.8 - - + +
400A SER* 1.3 82.8 - - - +
402A LYS* 1.4 64.4 - - + +
404A SER* 3.3 19.4 + - - +
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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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344A PRO* 5.8 7.2 - - + -
393A THR* 3.8 22.7 - - + -
398A MET* 3.0 34.2 + - + +
399A PHE* 4.0 2.7 - - - +
401A MET* 1.4 77.5 - - + +
403A THR* 1.3 64.1 + - + +
404A SER 3.4 6.8 - - - +
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Residues in contact with THR 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 PHE* 2.7 59.1 + - + +
400A SER* 2.8 18.4 + - - -
402A LYS* 1.3 76.3 - - + +
404A SER* 1.3 61.4 + - - +
405A SER 3.8 1.0 + - - -
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Residues in contact with SER 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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400A SER* 3.1 19.9 + - - -
401A MET* 3.4 15.7 - - - +
402A LYS 3.3 7.0 - - - +
403A THR* 1.3 78.7 + - - +
405A SER 1.3 49.0 + - - +
529A UNX 4.6 2.7 - - - -
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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