Contacts of the strand formed by residues 387 - 395 (chain A) in PDB entry 4XH9
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 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A GLY 4.7 4.1 + - - +
361A GLU* 4.4 12.7 - - + +
362A CYS* 4.1 21.2 - - + +
365A TYR* 3.8 24.5 - - + -
385A LYS 4.3 0.2 + - - -
386A VAL* 1.3 73.4 - - - +
388A LEU* 1.3 65.3 + - - +
389A CYS* 3.8 10.5 - - - +
390A HIS* 3.6 32.5 - - + +
404A PHE* 4.0 15.5 - - + -
405A LEU 3.5 24.7 - - - +
406A PHE* 3.8 21.8 - - + -
68B ARG* 4.0 16.5 + - - +
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Residues in contact with LEU 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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386A VAL* 3.7 9.8 + - + -
387A LEU* 1.3 73.4 - - - +
389A CYS* 1.3 60.9 + - + +
405A LEU* 2.8 24.3 + - + +
406A PHE 4.2 2.9 - - - +
407A GLN* 3.7 45.3 - - - +
491A GLN* 5.8 0.5 + - - -
495A CYS* 4.3 14.7 - - + +
499A ALA* 3.7 31.0 - - + +
68B ARG* 3.7 29.6 + - - +
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Residues in contact with CYS 389 (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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387A LEU* 3.4 3.0 - - - +
388A LEU* 1.3 81.8 - - - +
390A HIS* 1.3 65.4 + - - +
405A LEU* 2.7 38.9 + - + +
491A GLN* 3.3 26.7 - - - -
492A TRP* 3.7 39.6 - - + -
495A CYS* 3.9 20.6 - - + -
105B HIS* 3.9 9.2 - - - -
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Residues in contact with HIS 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 GLU* 2.9 24.2 + - - -
365A TYR* 3.4 24.4 - + - -
387A LEU* 3.6 27.4 - - + -
389A CYS* 1.3 78.5 - - - +
391A GLY* 1.3 59.3 + - - +
402A TYR* 2.6 29.2 + + + -
403A ILE 3.2 12.8 - - - +
404A PHE* 3.6 18.6 - + + -
492A TRP* 3.8 5.8 - - - -
105B HIS* 2.9 20.0 + - - -
106B PHE* 5.6 10.0 - + - -
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Residues in contact with GLY 391 (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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390A HIS* 1.3 77.0 - - - +
392A GLU* 1.3 65.5 + - - -
393A LEU 4.0 0.3 + - - -
402A TYR* 3.5 20.8 - - - -
403A ILE* 2.9 29.9 + - - +
492A TRP* 3.6 13.3 - - - -
105B HIS* 4.3 5.8 - - - -
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Residues in contact with GLU 392 (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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391A GLY* 1.3 73.3 - - - -
393A LEU* 1.3 72.6 + - - +
400A LYS* 4.5 29.6 + - + +
401A LEU 3.1 11.7 - - - +
402A TYR* 3.3 31.1 - - + -
415A PRO* 5.3 6.2 - - + +
484A ASN* 5.0 2.1 + - - +
488A HIS* 4.1 12.3 - - - -
492A TRP* 4.5 0.5 + - - -
105B HIS* 5.5 0.6 - - - -
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Residues in contact with LEU 393 (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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391A GLY 4.0 0.2 + - - -
392A GLU* 1.3 83.1 - - - +
394A ARG* 1.3 62.1 + - - +
400A LYS* 3.7 8.6 - - - +
401A LEU* 2.8 32.4 + - - +
403A ILE* 4.0 16.6 - - + +
466A PHE* 3.9 21.5 - - + -
481A LEU* 3.9 22.4 - - + -
482A GLN 3.6 16.8 - - - +
483A ALA* 3.7 16.8 - - + -
488A HIS* 4.0 2.2 - - + -
492A TRP* 3.5 51.6 - - + +
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Residues in contact with ARG 394 (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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393A LEU* 1.3 71.9 - - - +
395A SER* 1.3 73.4 + - - +
398A GLY* 2.8 39.8 + - - +
399A HIS 3.7 3.4 - - - +
400A LYS* 3.6 38.6 - - + +
448A MET* 3.6 10.3 - - + +
481A LEU* 3.4 6.4 - - - -
482A GLN* 2.8 63.8 + - - +
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Residues in contact with SER 395 (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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393A LEU 3.8 1.0 + - - -
394A ARG* 1.3 81.7 - - - +
396A LYS* 1.3 60.2 + - - +
397A SER* 2.9 25.8 + - - -
398A GLY* 2.9 16.6 + - - -
399A HIS* 2.9 25.2 + - - +
401A LEU* 3.8 24.4 - - - +
414A ARG* 4.5 2.2 + - - -
427A TYR* 6.1 1.1 - - - -
448A MET* 3.4 8.5 - - - +
479A HIS* 6.2 1.1 - - - -
480A THR 3.6 8.1 - - - -
481A LEU* 4.3 3.3 - - - +
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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