Contacts of the strand formed by residues 420 - 429 (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 PRO 420 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91D LEU* 4.5 7.2 - - + -
92D CYS* 4.3 8.3 - - + +
94D ILE* 4.2 12.1 - - + -
97D TRP* 3.6 5.3 - - + -
354D PHE* 3.5 38.1 - - + -
356D TYR* 3.5 23.3 - - - +
410D PHE 4.2 1.1 - - - +
411D VAL* 5.1 1.6 - - + -
418D ILE 3.5 8.3 - - - +
419D ARG* 1.3 86.3 - - + +
421D CYS* 1.3 55.2 + - - +
448D GLY* 2.6 46.5 + - - -
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Residues in contact with CYS 421 (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* 4.4 2.2 - - - -
354D PHE* 3.5 9.1 - - - -
410D PHE* 2.9 51.2 + - + +
412D GLN* 3.1 27.1 - - - -
419D ARG* 3.9 2.0 - - - -
420D PRO* 1.3 75.4 - - - +
422D PHE* 1.3 62.9 + - - +
446D PHE 3.0 15.5 - - - +
447D CYS* 2.1 43.7 - - - +
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Residues in contact with PHE 422 (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* 3.6 36.1 - + - -
352D PHE* 3.2 37.9 - + + -
374D PHE* 3.7 12.1 - + - -
376D MET* 3.5 30.3 - - + -
397D ILE* 4.1 6.5 - - + -
408D GLY 3.2 14.6 - - - +
410D PHE* 3.5 6.1 - - - -
421D CYS* 1.3 75.0 - - - +
423D TRP* 1.3 67.6 + - - +
424D VAL* 3.7 19.7 - - + -
445D SER* 3.2 4.9 - - - -
446D PHE* 2.9 61.5 + + + -
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Residues in contact with TRP 423 (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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119D GLU 5.5 0.2 - - - -
120D PRO* 3.0 32.1 - - + -
121D PHE* 3.4 17.6 - - + +
122D ILE* 3.6 30.0 + - + +
227D GLU 3.8 9.4 - - - -
228D SER* 4.2 1.7 - - - -
350D LYS* 3.9 10.5 - - + -
406D TYR* 3.6 23.6 - + + -
407D SER* 3.1 44.9 - - - -
408D GLY* 3.0 44.3 + - - -
409D SER 4.1 6.7 + - - +
410D PHE* 3.8 12.8 - + + -
422D PHE* 1.3 74.6 - - - +
424D VAL* 1.3 72.7 + - - +
425D GLU* 3.8 10.5 - - + -
443D SER* 5.7 5.2 - - - -
444D ILE 3.2 12.8 - - - +
445D SER* 4.1 8.1 - - - -
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Residues in contact with VAL 424 (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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374D PHE* 4.0 34.8 - - + -
397D ILE* 4.6 1.1 - - + -
398D VAL* 5.3 0.7 - - + -
404D SER* 4.8 2.0 - - - -
405D GLY 4.7 4.7 - - - +
406D TYR 3.5 9.9 - - - +
407D SER* 4.2 1.8 - - - -
422D PHE* 3.7 24.9 - - + -
423D TRP* 1.3 84.5 - - - +
425D GLU* 1.3 71.2 + - - +
426D LEU* 3.8 14.6 + - + +
442D SER 3.7 0.2 - - - +
443D SER* 3.2 6.8 - - - -
444D ILE* 2.7 53.7 + - + +
446D PHE* 5.2 0.2 - - + -
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Residues in contact with GLU 425 (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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118D ARG* 2.7 33.9 + - - -
119D GLU 3.0 19.8 + - - -
120D PRO* 3.3 27.7 - - + +
404D SER 3.2 1.4 - - - +
405D GLY* 3.1 26.3 + - - -
406D TYR* 2.7 44.6 + - + +
423D TRP* 3.8 2.9 - - + -
424D VAL* 1.3 75.1 - - - +
426D LEU* 1.3 63.1 + - - +
427D ILE* 3.2 22.4 - - + +
441D GLY* 4.8 6.3 - - - -
442D SER 3.4 7.0 - - - +
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Residues in contact with LEU 426 (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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102D LYS* 4.9 1.1 - - - +
106D ILE* 4.1 3.6 - - - +
398D VAL* 4.4 10.1 - - + -
403D TRP 3.8 18.8 - - - +
404D SER* 4.0 6.1 - - - -
424D VAL* 4.1 21.5 - - + +
425D GLU* 1.3 77.4 - - - +
427D ILE* 1.3 61.5 + - - +
428D ARG* 3.6 3.3 + - - +
441D GLY* 3.1 5.8 - - - -
442D SER* 2.7 46.6 + - - +
444D ILE* 4.2 23.1 - - + -
458D TRP 3.9 6.3 - - - +
459D PRO* 3.5 8.1 - - + +
460D ASP* 3.3 43.3 - - + +
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Residues in contact with ILE 427 (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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118D ARG* 3.7 24.5 - - - +
371D ARG* 3.8 22.2 - - + +
403D TRP* 3.4 17.9 + - - +
404D SER 3.1 13.3 + - - +
405D GLY* 4.1 11.7 - - - -
425D GLU* 3.2 34.8 - - - +
426D LEU* 1.3 69.5 - - - +
428D ARG* 1.3 78.4 + - - +
429D GLY 4.4 0.4 + - - +
430D ARG 4.5 7.4 - - - +
431D PRO* 6.1 0.4 - - + -
433D GLU* 4.6 0.2 - - - +
439D THR* 4.1 15.9 - - + -
440D SER 3.6 10.5 - - - +
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Residues in contact with ARG 428 (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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106D ILE* 3.7 19.7 - - + -
403D TRP* 3.6 20.0 - - - -
426D LEU 3.6 1.1 + - - +
427D ILE* 1.3 89.4 - - - +
429D GLY* 1.3 60.5 + - - +
433D GLU* 2.8 37.6 + - - +
438D TRP* 3.6 8.8 - - + -
439D THR* 3.5 2.3 - - - -
440D SER 3.0 31.7 + - - +
460D ASP* 2.7 53.4 + - + +
461D GLY 4.4 1.8 - - - +
462D ALA* 2.7 31.9 + - - +
463D GLU* 4.6 0.2 - - - +
464D LEU* 3.5 26.2 - - + +
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Residues in contact with GLY 429 (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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427D ILE* 5.5 1.0 - - - +
428D ARG* 1.3 73.9 - - - +
430D ARG* 1.3 67.2 + - - -
432D LYS* 3.4 4.2 + - - +
433D GLU* 2.9 38.0 + - - +
436D THR* 3.2 21.1 - - - -
438D TRP* 3.2 7.2 - - - -
464D LEU* 3.6 7.7 - - - +
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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