Contacts of the strand formed by residues 387 - 395 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358D GLY 4.8 3.9 + - - +
361D GLU* 4.4 12.7 - - + +
362D CYS* 4.1 15.3 - - + +
365D TYR* 3.8 25.6 - - + -
386D VAL* 1.3 73.5 - - - +
388D LEU* 1.3 64.1 + - - +
389D CYS* 3.9 5.7 - - - +
390D HIS* 3.5 32.5 - - + -
404D PHE* 4.0 14.4 - - + -
405D LEU 3.5 34.1 - - - +
406D PHE* 3.7 23.8 - - + -
68E ARG* 4.5 14.8 + - - +
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Residues in contact with LEU 388 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386D VAL* 3.7 14.3 - - + -
387D LEU* 1.3 72.0 - - - +
389D CYS* 1.3 61.2 + - + +
405D LEU* 2.8 25.4 + - + +
406D PHE 4.1 4.0 - - - +
407D GLN* 3.5 47.8 - - - +
495D CYS* 4.3 14.2 - - - +
499D ALA* 3.7 31.0 - - + -
68E ARG* 4.1 20.4 + - - +
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Residues in contact with CYS 389 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387D LEU* 3.4 2.8 - - - +
388D LEU* 1.3 80.9 - - - +
390D HIS* 1.3 68.5 + - - +
405D LEU* 2.8 36.0 + - + +
491D GLN* 3.4 25.6 - - - -
492D TRP* 3.8 33.3 - - + -
495D CYS* 3.8 22.9 - - + -
105E HIS* 3.8 14.4 - - - -
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Residues in contact with HIS 390 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D GLU* 3.1 24.7 + - - -
365D TYR* 3.4 24.8 - + - -
387D LEU* 3.5 28.5 - - + -
389D CYS* 1.3 79.2 - - - +
391D GLY* 1.3 58.6 + - - +
402D TYR* 2.5 30.5 + + + -
403D ILE 3.1 13.7 - - - +
404D PHE* 3.7 18.8 - + + -
492D TRP* 3.7 7.2 - - - -
105E HIS* 3.0 20.0 + - - -
106E PHE* 5.6 10.3 - + - -
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Residues in contact with GLY 391 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390D HIS* 1.3 76.1 - - - +
392D GLU* 1.3 62.4 + - - -
393D LEU 3.9 0.2 + - - -
402D TYR* 3.5 24.5 - - - -
403D ILE* 2.9 28.0 + - - +
492D TRP* 3.5 13.4 - - - -
105E HIS* 4.3 6.5 - - - -
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Residues in contact with GLU 392 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D GLY* 1.3 72.4 - - - -
393D LEU* 1.3 72.3 + - - +
400D LYS* 3.2 42.8 + - + +
401D LEU 3.1 13.2 - - - +
402D TYR* 3.9 14.2 - - + -
484D ASN* 4.9 4.9 + - - +
488D HIS* 4.2 10.9 - - - -
492D TRP* 4.6 0.5 + - - -
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Residues in contact with LEU 393 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391D GLY 3.9 0.6 + - - -
392D GLU* 1.3 82.3 - - - +
394D ARG* 1.3 60.9 + - - +
395D SER 3.8 0.2 + - - -
400D LYS* 3.7 9.9 - - - +
401D LEU* 2.9 32.3 + - - +
403D ILE* 3.9 16.6 - - + -
466D PHE* 3.8 21.5 - - + -
481D LEU* 3.9 24.7 - - + -
482D GLN 3.6 17.7 - - - +
483D ALA* 3.8 15.9 - - + +
484D ASN* 5.7 0.4 - - - +
488D HIS* 4.0 3.1 - - + -
492D TRP* 3.6 50.0 - - + +
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Residues in contact with ARG 394 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D LEU* 1.3 72.1 - - - +
395D SER* 1.3 73.6 + - - +
398D GLY* 4.1 20.9 + - - +
399D HIS 3.8 2.9 - - - -
400D LYS* 3.7 32.7 - - - +
448D MET* 3.4 11.3 - - + +
481D LEU* 3.4 7.1 - - - -
482D GLN* 2.9 69.6 + - - +
483D ALA 5.2 3.0 + - - -
484D ASN* 5.5 3.0 + - - +
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Residues in contact with SER 395 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393D LEU 3.8 1.2 + - - -
394D ARG* 1.3 81.4 - - - +
396D LYS* 1.3 65.7 + - - +
397D SER* 3.6 9.0 + - - -
398D GLY* 3.0 12.3 + - - -
399D HIS* 2.8 44.6 + - - +
401D LEU* 3.8 25.1 - - - -
427D TYR* 6.1 1.3 - - - -
448D MET* 3.4 8.9 - - - +
479D HIS* 6.5 0.7 - - - -
480D THR 3.7 7.0 - - - -
481D LEU* 4.5 3.4 - - - -
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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