Contacts of the strand formed by residues 419 - 429 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92F CYS* 3.7 14.7 - - + +
94F ILE* 6.2 0.2 - - + -
411F VAL* 3.4 8.6 - - - +
412F GLN* 2.3 83.2 + - + +
413F THR* 4.5 7.5 - - - +
415F LEU* 4.3 24.0 - - + +
417F CYS 3.5 3.0 + - - -
418F ILE* 1.3 71.7 - - - +
420F PRO* 1.3 72.3 - - + +
421F CYS* 3.7 5.8 + - - -
447F CYS* 4.0 11.2 - - - +
448F GLY* 4.4 2.2 - - - +
449F VAL* 4.1 32.8 - - - +
210H ILE* 4.7 1.8 - - - +
211H ILE* 3.1 41.0 + - - +
212H THR* 5.5 1.4 - - - +
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Residues in contact with PRO 420 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F LEU* 4.4 7.4 - - + -
92F CYS* 4.3 9.9 - - + +
94F ILE* 3.9 22.7 - - + -
97F TRP* 3.3 5.8 - - + -
354F PHE* 3.6 38.1 - - + -
356F TYR* 3.3 25.6 - - + +
410F PHE 4.2 1.1 - - - +
411F VAL* 5.1 1.6 - - + -
418F ILE 3.7 8.1 - - - +
419F ARG* 1.3 85.6 - - + +
421F CYS* 1.3 55.5 + - - +
448F GLY 2.7 31.2 + - - -
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Residues in contact with CYS 421 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F TRP* 4.4 1.8 - - - -
354F PHE* 3.4 9.1 - - - -
410F PHE* 2.7 54.3 + - + +
412F GLN* 2.7 29.6 - - - -
419F ARG* 3.9 2.2 - - - -
420F PRO* 1.3 76.1 - - - +
422F PHE* 1.3 59.2 + - - +
446F PHE 3.0 16.4 - - - +
447F CYS* 2.1 41.3 - - - -
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Residues in contact with PHE 422 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F TRP* 3.6 40.8 - + - -
352F PHE* 3.3 37.2 - + + -
374F PHE* 4.0 10.3 - + - -
376F MET* 3.7 23.3 - - + -
397F ILE* 4.1 8.3 - - + -
408F GLY 3.3 10.8 - - - +
409F SER* 4.3 0.2 - - - -
410F PHE* 3.5 6.7 - - - -
421F CYS* 1.3 75.8 - - - +
423F TRP* 1.3 71.5 + - - +
424F VAL* 3.5 23.3 - - + -
445F SER* 3.1 4.0 - - - -
446F PHE* 2.9 62.6 + + + -
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Residues in contact with TRP 423 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F PRO* 3.2 31.2 - - + -
121F PHE* 3.4 17.9 - - + +
122F ILE* 3.4 40.6 + - + +
227F GLU 3.7 10.8 - - - -
228F SER* 4.1 2.8 - - - -
350F LYS* 3.7 11.7 - - + -
406F TYR* 3.4 21.5 - + + -
407F SER* 3.3 28.5 - - - -
408F GLY* 2.8 64.4 + - - +
409F SER 4.2 5.5 + - - +
410F PHE* 4.0 11.4 - + - -
422F PHE* 1.3 76.3 - - - +
424F VAL* 1.3 75.8 + - - +
425F GLU* 3.8 8.7 - - + -
443F SER* 5.4 5.2 - - - -
444F ILE 3.3 9.9 - - - +
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Residues in contact with VAL 424 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374F PHE* 4.1 35.7 - - + -
397F ILE* 4.5 2.0 - - + -
404F SER* 4.6 6.1 - - - -
405F GLY 4.8 0.2 - - - +
406F TYR 3.6 10.8 - - - +
407F SER* 4.5 0.9 - - - -
422F PHE* 3.5 26.2 - - + -
423F TRP* 1.3 85.6 - - - +
425F GLU* 1.3 68.5 + - - +
426F LEU* 3.9 14.4 + - + -
442F SER 3.5 0.2 - - - +
443F SER* 3.1 25.3 - - - -
444F ILE* 2.8 35.0 + - + +
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Residues in contact with GLU 425 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ARG* 2.5 35.9 + - - -
119F GLU 2.9 16.5 + - - -
120F PRO* 3.1 27.6 - - + +
404F SER* 3.0 23.6 - - - +
405F GLY* 3.0 5.9 + - - -
406F TYR* 2.7 56.6 + - + +
423F TRP* 3.8 3.4 - - + -
424F VAL* 1.3 71.0 - - - +
426F LEU* 1.3 63.7 + - - +
427F ILE* 3.8 13.6 - - + +
441F GLY* 4.7 5.6 - - - -
442F SER 3.2 7.2 - - - +
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Residues in contact with LEU 426 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102F LYS* 4.9 0.9 - - - +
106F ILE* 4.0 4.9 - - - +
398F VAL* 4.2 8.3 - - + -
403F TRP 3.6 19.1 - - - +
404F SER* 3.6 10.3 - - - +
424F VAL* 4.1 17.9 - - + +
425F GLU* 1.3 75.0 - - - +
427F ILE* 1.3 63.8 + - - +
428F ARG* 3.6 1.9 + - - +
441F GLY* 3.2 4.2 - - - -
442F SER* 2.7 44.9 + - - +
444F ILE* 4.2 22.7 - - + -
458F TRP 3.7 8.7 - - - +
459F PRO 3.5 6.7 - - - +
460F ASP* 3.1 45.5 - - + +
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Residues in contact with ILE 427 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F ARG* 4.0 16.4 - - - +
371F ARG* 4.0 29.2 - - + +
403F TRP* 3.5 16.5 - - - +
404F SER* 2.9 15.3 + - - +
405F GLY* 3.8 20.2 - - - -
425F GLU* 3.8 27.4 - - - +
426F LEU* 1.3 70.9 - - - +
428F ARG* 1.3 77.1 + - - +
429F GLY 5.5 0.7 - - - +
430F ARG 4.6 7.0 - - - +
431F PRO* 6.1 1.1 - - + -
433F GLU* 4.3 0.2 - - - +
439F THR* 4.2 20.4 - - + -
440F SER 3.4 10.1 - - - +
441F GLY* 4.3 0.7 - - - -
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Residues in contact with ARG 428 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F ILE* 3.5 29.8 - - + -
403F TRP* 3.5 19.0 - - - -
426F LEU 4.2 1.1 - - - +
427F ILE* 1.3 87.6 - - - +
429F GLY* 1.3 59.9 + - - +
433F GLU* 2.9 34.5 + - - +
438F TRP* 3.4 10.9 - - + -
439F THR* 3.6 0.9 - - - -
440F SER 2.7 34.7 + - - +
460F ASP* 2.9 37.7 + - + +
461F GLY 4.3 1.8 - - - +
462F ALA* 2.7 32.9 + - - +
463F GLU* 4.5 0.4 - - - +
464F LEU* 3.4 27.1 - - + +
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Residues in contact with GLY 429 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427F ILE* 5.0 1.1 - - - +
428F ARG* 1.3 73.4 - - - +
430F ARG* 1.3 67.9 + - - -
432F LYS* 3.5 4.2 + - - +
433F GLU* 2.8 43.1 + - - +
436F THR* 3.3 10.5 - - - -
438F TRP* 3.2 12.8 - - - -
464F LEU* 3.9 5.9 - - - +
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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