Contacts of the strand formed by residues 419 - 429 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210F ILE* 4.8 1.4 - - - +
211F ILE* 2.9 43.6 + - - +
212F THR* 5.3 2.2 - - - +
92G CYS* 3.7 13.0 - - - +
411G VAL* 3.6 8.3 - - - +
412G GLN* 3.1 64.3 + - + +
413G THR* 5.1 3.4 - - + +
415G LEU* 3.8 29.8 - - + +
417G CYS 3.4 4.2 + - - -
418G ILE* 1.3 71.5 - - - +
420G PRO* 1.3 78.2 - - + +
421G CYS* 3.9 5.1 - - - -
447G CYS* 4.0 15.3 - - - +
448G GLY* 4.4 2.7 - - - +
449G VAL* 4.5 26.1 - - - +
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Residues in contact with PRO 420 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G LEU* 4.7 7.9 - - + -
92G CYS* 4.2 10.1 - - + +
94G ILE* 4.1 22.0 - - + -
97G TRP* 3.5 4.0 - - + -
354G PHE* 3.6 36.1 - - + -
356G TYR* 3.3 26.5 - - - +
410G PHE 4.2 1.3 - - - +
411G VAL* 5.2 1.6 - - + -
418G ILE 3.5 7.9 - - - +
419G ARG* 1.3 89.1 - - + +
421G CYS* 1.3 56.7 + - - +
447G CYS 3.6 0.2 - - - -
448G GLY* 2.7 33.1 + - - -
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Residues in contact with CYS 421 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G TRP* 4.3 1.8 - - - -
354G PHE* 3.4 10.9 - - - -
410G PHE* 2.9 47.9 + - + +
412G GLN* 3.4 24.7 - - - -
419G ARG* 3.9 4.7 - - - -
420G PRO* 1.3 76.1 - - - +
422G PHE* 1.3 67.9 + - - +
446G PHE 3.0 13.0 - - - +
447G CYS* 2.1 44.0 - - - +
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Residues in contact with PHE 422 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G TRP* 3.8 30.5 - + - -
352G PHE* 3.5 33.0 - + + -
374G PHE* 3.8 10.8 - + - -
376G MET* 3.7 27.4 - - + -
397G ILE* 3.9 9.4 - - + -
408G GLY 3.3 14.1 - - - +
410G PHE* 3.6 7.9 - - - -
421G CYS* 1.3 77.2 - - - +
423G TRP* 1.3 71.3 + - - +
424G VAL* 3.5 22.2 - - + -
445G SER* 3.1 1.6 - - - -
446G PHE* 2.8 70.0 + + + -
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Residues in contact with TRP 423 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G PRO* 3.3 25.1 - - + -
121G PHE* 3.5 21.4 - - + +
122G ILE* 3.5 37.1 + - + +
227G GLU 4.0 1.3 - - - -
228G SER* 4.2 1.9 - - - -
350G LYS* 3.6 22.0 - - + -
406G TYR* 3.3 33.2 - + + -
407G SER* 3.4 18.1 - - - -
408G GLY* 3.0 50.1 + - - +
409G SER 3.9 7.3 + - - -
410G PHE* 4.1 11.7 - + - -
422G PHE* 1.3 75.6 - - - +
424G VAL* 1.3 78.6 + - - +
425G GLU* 3.7 8.5 - - + -
443G SER* 5.6 4.9 - - - -
444G ILE 3.1 12.8 - - - +
445G SER* 3.9 0.4 - - - +
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Residues in contact with VAL 424 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374G PHE* 3.9 36.3 - - + -
397G ILE* 4.5 0.7 - - + -
398G VAL* 5.4 0.2 - - + -
404G SER* 4.6 7.0 - - - -
405G GLY 4.6 0.7 - - - +
406G TYR 3.5 9.6 - - - +
407G SER* 4.6 0.4 - - - -
422G PHE* 3.5 25.1 - - + -
423G TRP* 1.3 86.7 - - - +
425G GLU* 1.3 73.2 + - - +
426G LEU* 3.8 12.6 + - + +
443G SER* 3.3 8.5 - - - -
444G ILE* 2.8 49.5 + - + +
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Residues in contact with GLU 425 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G ARG* 2.5 51.2 + - - -
119G GLU 3.0 16.8 + - - -
120G PRO* 3.2 26.4 - - + +
404G SER 3.0 1.6 - - - -
405G GLY* 3.0 26.5 + - - -
406G TYR* 2.6 40.2 + - + +
423G TRP* 3.7 2.3 - - + -
424G VAL* 1.3 74.6 - - - +
426G LEU* 1.3 66.8 + - - +
427G ILE* 3.5 13.7 - - + +
441G GLY* 4.6 5.7 - - - -
442G SER 3.4 6.1 - - - +
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Residues in contact with LEU 426 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102G LYS* 5.1 1.6 - - - +
106G ILE* 4.2 3.1 - - - +
398G VAL* 4.6 7.2 - - + -
403G TRP 4.0 15.9 - - - +
404G SER* 3.7 7.0 - - - +
424G VAL* 4.0 18.8 - - + +
425G GLU* 1.3 80.9 - - - +
427G ILE* 1.3 62.4 + - - +
428G ARG* 3.7 2.5 + - - +
441G GLY* 3.1 5.3 - - - -
442G SER* 2.7 49.5 + - - +
443G SER* 4.6 1.3 - - - +
444G ILE* 4.1 21.5 - - + -
458G TRP 3.9 7.9 - - - +
459G PRO* 3.4 9.0 - - + +
460G ASP* 3.1 45.8 - - + +
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Residues in contact with ILE 427 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118G ARG* 3.6 21.5 - - - +
371G ARG* 3.8 25.4 - - + +
403G TRP* 3.4 17.4 - - + +
404G SER 3.0 14.4 + - - +
405G GLY* 4.1 10.8 - - - -
425G GLU* 3.5 32.1 - - + +
426G LEU* 1.3 70.5 - - - +
428G ARG* 1.3 77.8 + - - +
429G GLY 5.7 0.2 - - - +
430G ARG 4.5 7.4 - - - +
431G PRO* 5.9 1.8 - - + -
433G GLU* 4.4 0.2 - - - +
439G THR* 4.2 18.6 - - + -
440G SER 3.5 9.4 - - - +
441G GLY* 4.4 0.2 - - - -
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Residues in contact with ARG 428 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G ILE* 3.6 19.5 - - + -
403G TRP* 3.7 18.3 - - - -
426G LEU 3.7 1.8 + - - +
427G ILE* 1.3 86.9 - - - +
429G GLY* 1.3 58.8 + - - +
433G GLU* 2.6 39.9 + - - -
438G TRP* 3.7 8.1 - - + -
439G THR* 3.5 3.5 - - - +
440G SER 3.0 31.6 + - - -
460G ASP* 2.9 48.1 + - + +
461G GLY 4.4 2.2 - - - +
462G ALA* 2.8 28.4 + - - +
463G GLU* 4.8 0.2 - - - +
464G LEU* 3.1 29.6 - - + +
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Residues in contact with GLY 429 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G ILE* 5.7 0.3 - - - +
428G ARG* 1.3 74.1 - - - +
430G ARG* 1.3 62.6 + - - -
432G LYS* 3.5 3.1 + - - +
433G GLU* 2.7 47.8 + - - +
436G THR* 3.2 20.2 - - - -
438G TRP* 3.3 6.5 - - - -
464G LEU* 3.7 6.7 - - - +
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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