Contacts of the strand formed by residues 386 - 390 (chain A) in PDB entry 6CM1
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 LYS 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A PHE* 3.8 7.6 - - - +
383A LYS 3.3 29.0 + - - +
384A GLY 4.5 0.2 - - - +
385A ASP* 1.4 71.9 + - - +
387A HIS* 1.3 65.7 + - - +
388A TRP* 3.8 21.5 - - + -
400A PRO* 4.8 10.5 - - + -
401A LYS* 3.3 10.8 - - - +
402A HIS* 3.3 48.2 + - + +
403A ILE* 4.4 1.7 - - - +
649A PX4 4.5 9.9 - - - -
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Residues in contact with HIS 387 (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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380A VAL* 4.0 20.4 - - + -
381A PHE 3.1 12.8 - - - +
382A PHE* 3.5 24.2 - + + -
386A LYS* 1.3 77.3 - - - +
388A TRP* 1.4 63.4 + - - +
389A VAL* 4.2 4.8 - - + +
399A TYR* 3.6 24.5 + + - -
400A PRO* 3.5 2.1 - - - +
401A LYS* 2.6 69.3 + - + -
402A HIS 3.3 21.1 + - - -
403A ILE* 4.3 2.0 - - + -
405A GLU 4.0 2.0 + - - -
406A LEU* 3.8 35.0 + - + +
443A ARG* 5.4 0.4 + - - -
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Residues in contact with TRP 388 (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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363A GLY 3.6 18.4 + - - -
364A LEU* 4.0 19.3 - - + -
365A PRO* 3.3 32.8 - - + +
368A ILE* 5.3 0.4 - - + -
379A PHE 3.8 0.5 - - - +
380A VAL* 3.4 3.6 - - - +
381A PHE* 2.9 41.0 + - + +
383A LYS* 3.5 42.4 - - + -
386A LYS* 3.8 24.5 - - + -
387A HIS* 1.4 71.6 - - - +
389A VAL* 1.4 64.6 + - - +
390A PHE* 3.8 11.7 - + + -
395A LEU* 3.7 27.6 - - + -
399A TYR* 4.6 2.2 - - - -
400A PRO* 3.6 32.2 - - + +
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Residues in contact with VAL 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ARG* 4.6 10.5 - - - +
378A LYS* 3.6 31.6 - - + -
379A PHE 3.4 5.4 - - - +
380A VAL* 3.9 18.4 - - + -
387A HIS* 4.2 9.2 - - + +
388A TRP* 1.4 76.0 - - - +
390A PHE* 1.3 52.9 + - - +
395A LEU* 3.3 8.1 - - - +
396A GLU* 2.7 57.3 + - + +
399A TYR* 3.6 36.3 - - + +
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Residues in contact with PHE 390 (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 TRP* 3.5 54.7 - + + -
362A ARG 4.4 8.3 - - - -
363A GLY* 3.7 7.0 - - - -
364A LEU* 3.5 49.8 - - + -
378A LYS* 3.7 5.4 - - - +
379A PHE* 2.9 31.5 + - + +
381A PHE* 3.9 22.7 - + + -
388A TRP* 3.8 5.8 - + + -
389A VAL* 1.3 73.2 - - - +
391A ASP* 1.4 57.6 + - - +
394A SER* 3.9 5.6 - - - -
395A LEU* 3.4 47.6 - - + -
396A GLU* 3.9 2.9 - - - -
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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