Contacts of the strand formed by residues 419 - 429 (chain E) 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 ARG 419 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92E CYS* 3.6 13.6 - - + +
411E VAL* 3.5 7.3 - - - +
412E GLN* 2.8 69.2 + - + +
413E THR* 4.6 8.4 - - - +
415E LEU* 3.9 28.0 - - + +
417E CYS 3.6 1.2 + - - -
418E ILE* 1.3 72.9 - - - +
420E PRO* 1.3 67.1 - - + +
421E CYS* 3.7 12.2 + - - -
447E CYS* 4.1 7.0 - - - +
448E GLY* 4.1 7.6 - - - +
449E VAL* 4.3 26.1 - - - +
210G ILE* 4.8 1.8 - - - +
211G ILE* 2.9 46.2 + - - +
212G THR* 5.2 2.2 - - - +
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Residues in contact with PRO 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91E LEU* 4.2 8.7 - - + -
92E CYS* 4.3 6.5 - - + +
94E ILE* 4.0 22.2 - - + -
97E TRP* 3.2 6.9 - - + -
354E PHE* 3.5 39.5 - - + -
356E TYR* 3.3 25.6 - - - +
410E PHE 4.2 1.6 - - - +
411E VAL* 5.1 1.8 - - + -
418E ILE 3.5 8.7 - - - +
419E ARG* 1.3 85.8 - - + +
421E CYS* 1.3 60.0 + - - +
448E GLY 2.9 23.2 + - - -
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Residues in contact with CYS 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E TRP* 4.3 1.3 - - - -
354E PHE* 3.5 9.8 - - - -
410E PHE* 3.0 45.8 + - + +
412E GLN* 2.8 29.2 - - - -
419E ARG* 3.9 3.6 - - - -
420E PRO* 1.3 77.5 - - - +
422E PHE* 1.3 64.0 + - - +
446E PHE 3.0 17.0 - - - +
447E CYS* 2.1 43.7 - - - +
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Residues in contact with PHE 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E TRP* 3.7 39.0 - + - -
352E PHE* 3.3 37.9 - + + -
354E PHE* 4.7 0.2 - - + -
374E PHE* 3.9 9.9 - + - -
376E MET* 3.7 23.8 - - + -
397E ILE* 4.0 9.2 - - + -
408E GLY 3.3 10.5 - - - +
410E PHE* 3.7 7.2 - - - -
421E CYS* 1.3 75.7 - - - +
423E TRP* 1.3 69.6 + - - +
424E VAL* 3.6 21.8 - - + -
445E SER* 3.4 1.9 - - - -
446E PHE* 2.9 64.6 + + + +
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Residues in contact with TRP 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E PRO* 3.2 27.8 - - + -
121E PHE* 3.4 22.8 - - + +
122E ILE* 3.5 42.7 + - + +
227E GLU 3.8 1.8 - - - -
228E SER* 4.1 3.1 - - - -
229E GLU 5.6 0.2 - - - +
350E LYS* 3.6 21.3 - - + -
406E TYR* 3.6 17.0 - + + -
407E SER* 3.3 26.8 - - - -
408E GLY* 2.9 60.0 + - - +
409E SER 4.2 4.8 + - - +
410E PHE* 4.0 12.6 - + + -
422E PHE* 1.3 77.9 - - - +
424E VAL* 1.3 81.5 + - - +
425E GLU* 4.0 7.2 - - + -
443E SER* 5.6 4.3 - - - -
444E ILE 3.4 8.7 - - - +
445E SER* 4.1 0.2 - - - -
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Residues in contact with VAL 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374E PHE* 3.9 37.2 - - + -
397E ILE* 4.7 0.2 - - + -
398E VAL* 5.1 0.2 - - + -
404E SER* 4.6 6.1 - - - -
406E TYR 3.7 7.4 - - - +
407E SER* 4.1 0.9 - - - -
422E PHE* 3.6 24.2 - - + -
423E TRP* 1.3 87.9 - - - +
425E GLU* 1.3 68.2 + - - +
426E LEU* 3.6 21.9 - - + +
443E SER* 3.1 7.8 - - - -
444E ILE* 3.0 49.0 + - + +
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Residues in contact with GLU 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E ARG* 2.7 33.3 + - - -
119E GLU 2.9 17.9 + - - -
120E PRO* 3.1 25.5 - - + +
404E SER* 3.0 23.6 - - - +
405E GLY* 3.2 4.5 + - - -
406E TYR* 2.9 40.8 + - - +
423E TRP* 3.9 5.5 - - + -
424E VAL* 1.3 75.0 - - - +
426E LEU* 1.3 65.3 + - - +
427E ILE* 3.5 19.4 - - + +
441E GLY* 4.5 5.9 - - - -
442E SER 3.2 9.0 - - - +
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Residues in contact with LEU 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LYS* 5.0 0.9 - - - +
106E ILE* 4.4 0.2 - - - +
398E VAL* 4.7 5.4 - - + -
403E TRP 4.2 16.2 - - - +
404E SER* 3.6 7.0 - - - +
424E VAL* 3.6 21.5 - - + +
425E GLU* 1.3 79.9 - - - +
427E ILE* 1.3 63.0 + - - +
428E ARG* 3.5 9.0 + - + +
441E GLY* 3.3 4.3 - - - -
442E SER* 2.9 41.8 + - - +
443E SER* 4.5 0.9 - - - +
444E ILE* 4.0 21.3 - - + -
458E TRP 3.8 8.5 - - - +
459E PRO* 3.5 9.2 - - + +
460E ASP* 3.2 44.6 - - + +
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Residues in contact with ILE 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118E ARG* 3.9 22.2 - - - +
371E ARG* 4.1 21.3 - - + +
403E TRP* 3.5 17.5 - - - +
404E SER 2.8 15.4 + - - +
405E GLY* 3.7 17.3 - - - -
406E TYR 4.3 0.7 - - - +
425E GLU* 3.5 32.1 - - - +
426E LEU* 1.3 69.6 - - - +
428E ARG* 1.3 72.8 + - - +
429E GLY 4.4 0.8 + - - +
430E ARG 4.5 7.2 - - - +
431E PRO* 6.0 1.3 - - + -
433E GLU* 4.4 0.5 - - - +
439E THR* 4.2 21.8 - - + -
440E SER 3.5 9.4 - - - +
441E GLY* 4.3 0.2 - - - -
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Residues in contact with ARG 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E ILE* 3.6 25.1 - - + -
403E TRP* 3.6 18.0 - - - -
426E LEU* 4.0 3.8 - - - +
427E ILE* 1.3 85.6 - - - +
429E GLY* 1.3 59.9 + - - +
433E GLU* 2.6 37.7 + - - +
438E TRP* 3.6 7.4 - - + -
439E THR* 3.5 2.9 - - - +
440E SER 2.8 32.5 + - - +
460E ASP* 2.9 41.3 + - - +
461E GLY* 4.5 2.0 - - - +
462E ALA* 2.8 32.5 + - - +
464E LEU* 3.3 28.7 - - + +
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Residues in contact with GLY 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427E ILE* 4.4 1.6 + - - +
428E ARG* 1.3 74.4 - - - +
430E ARG* 1.3 67.8 + - - -
432E LYS* 3.3 4.9 + - - +
433E GLU* 2.7 42.8 + - - +
436E THR* 3.2 20.2 - - - -
438E TRP* 3.3 6.1 - - - -
464E LEU* 3.7 5.7 - - - +
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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