Contacts of the strand formed by residues 372 - 379 (chain D) in PDB entry 2HU4
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 SER 372 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365D THR* 3.6 0.9 - - - -
366D LYS* 3.0 19.9 + - - +
367D SER* 3.0 21.9 + - - -
370D SER* 2.6 32.5 + - - -
371D ARG* 1.3 73.6 - - - +
373D GLY* 1.3 63.7 + - - +
400D ILE* 3.5 21.3 - - - -
402D ASP 3.5 7.6 - - - -
403D TRP* 3.4 15.6 - - - -
404D SER* 3.5 0.4 + - - -
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Residues in contact with GLY 373 (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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365D THR* 3.1 9.0 - - - -
366D LYS* 3.5 9.6 - - - -
372D SER* 1.3 74.2 - - - +
374D PHE* 1.3 60.8 + - - +
398D VAL* 3.1 18.8 - - - -
399D ALA 3.3 14.0 + - - -
402D ASP 2.9 14.6 + - - -
404D SER* 2.9 23.5 + - - -
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Residues in contact with PHE 374 (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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352D PHE* 3.9 2.2 - + - -
363D GLY* 3.6 13.7 - - - -
364D ARG* 3.0 48.2 - - - -
365D THR* 3.9 8.1 - - + +
366D LYS* 3.4 6.4 + - - +
373D GLY* 1.3 75.2 - - - +
375D GLU* 1.3 77.6 + - - +
376D MET* 4.1 2.0 - - - -
396D ASP 4.1 0.2 - - - -
397D ILE* 3.1 17.3 + - + -
398D VAL* 2.8 45.3 + - + +
404D SER* 4.6 5.8 - - - -
405D GLY 4.9 4.9 - - - -
407D SER* 3.5 37.2 - - - -
422D PHE* 3.7 22.7 - + - -
424D VAL* 4.0 20.2 - - + -
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Residues in contact with GLU 375 (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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327D ARG* 5.2 0.2 + - - -
362D ILE 3.4 2.8 - - - +
363D GLY* 3.5 2.1 - - - -
364D ARG* 2.8 56.8 + - + +
365D THR 4.4 2.5 - - - +
366D LYS* 2.9 38.8 + - + +
374D PHE* 1.3 82.5 - - - +
376D MET* 1.3 66.1 + - - +
377D ILE* 3.1 18.0 - - + +
394D LYS* 2.6 35.8 + - + -
395D GLN 3.5 12.8 - - - +
396D ASP* 4.4 3.1 - - - +
397D ILE* 4.2 2.0 - - - +
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Residues in contact with MET 376 (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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97D TRP* 3.5 49.8 - - + +
352D PHE* 3.7 17.3 - - + -
361D TRP* 4.0 16.0 - - + -
362D ILE 3.2 9.9 - - - +
363D GLY* 3.4 21.3 - - - -
374D PHE* 4.1 2.5 - - - -
375D GLU* 1.3 74.8 - - - +
377D ILE* 1.3 65.3 + - - +
392D VAL 3.9 0.2 - - - +
394D LYS* 3.4 1.6 - - - +
395D GLN* 2.9 38.5 + - + +
397D ILE* 3.8 11.9 - - + -
422D PHE* 3.5 37.5 - - + -
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Residues in contact with ILE 377 (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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321D VAL* 3.7 22.0 - - + -
360D VAL 3.4 2.3 - - - +
361D TRP* 3.3 6.3 - - - -
362D ILE* 2.7 48.0 + - + +
364D ARG* 3.4 24.7 - - + +
375D GLU* 3.1 29.8 - - + +
376D MET* 1.3 80.7 - - - +
378D TRP* 1.3 65.3 + - - +
379D ASP* 3.7 3.3 + - + +
390D PHE* 3.7 37.2 - - + -
392D VAL 3.4 3.4 - - - +
394D LYS* 4.1 17.5 - - + +
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Residues in contact with TRP 378 (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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356D TYR* 3.8 26.7 - + + -
359D GLY* 3.8 11.9 - - - -
360D VAL* 3.1 45.1 - - - -
361D TRP* 3.6 49.8 - + + -
377D ILE* 1.3 74.1 - - - +
379D ASP* 1.3 56.7 + - - +
380D PRO* 3.2 26.5 - - + +
381D ASN* 5.4 1.3 - - - -
390D PHE* 3.6 0.2 - - - +
391D SER* 3.1 42.4 + - - -
392D VAL* 3.0 24.2 + - + +
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Residues in contact with ASP 379 (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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319D SER* 2.7 28.6 + - - +
321D VAL* 4.4 2.8 - - + +
360D VAL* 3.0 30.7 + - + -
362D ILE* 5.1 2.5 - - + -
377D ILE* 3.7 5.8 + - + -
378D TRP* 1.3 72.0 - - - +
380D PRO* 1.3 78.8 - - - +
381D ASN 2.8 6.4 + - - +
382D GLY* 3.2 20.9 + - - -
387D ASP* 3.8 11.4 - - - +
389D SER 3.1 23.7 - - - +
390D PHE* 3.9 11.0 - - + -
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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