Contacts of the strand formed by residues 419 - 429 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210E ILE* 4.7 1.2 - - - +
211E ILE* 2.9 45.9 + - - +
212E THR* 5.3 2.6 - - - +
92H CYS* 3.8 12.4 - - - +
411H VAL* 3.7 4.2 - - - +
412H GLN* 2.4 87.5 + - + +
413H THR* 4.8 5.1 - - - +
415H LEU* 3.8 29.9 - - + +
417H CYS 3.2 5.1 + - - -
418H ILE* 1.3 71.2 - - - +
420H PRO* 1.3 77.7 - - + +
421H CYS* 3.9 3.5 + - - -
447H CYS* 4.2 7.2 - - - +
448H GLY* 4.4 3.1 - - - +
449H VAL* 4.5 26.8 - - - +
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Residues in contact with PRO 420 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H LEU* 4.3 7.4 - - + -
92H CYS* 4.2 12.6 - - + +
94H ILE* 4.4 17.9 - - + -
97H TRP* 3.7 4.9 - - + -
354H PHE* 3.6 37.2 - - + -
356H TYR* 3.3 25.4 - - - +
410H PHE 4.4 1.1 - - - +
411H VAL* 5.1 1.8 - - + -
418H ILE 3.4 8.3 - - - +
419H ARG* 1.3 88.2 - - + +
421H CYS* 1.3 56.5 + - - +
448H GLY* 2.7 33.2 + - - -
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Residues in contact with CYS 421 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H TRP* 4.2 2.2 - - - -
354H PHE* 3.3 11.8 - - - -
410H PHE* 3.0 44.9 + - + +
412H GLN* 2.9 28.9 - - - -
419H ARG* 4.0 1.3 - - - -
420H PRO* 1.3 76.3 - - - +
422H PHE* 1.3 64.9 + - - +
446H PHE 2.9 16.6 - - - +
447H CYS* 2.1 44.4 - - - +
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Residues in contact with PHE 422 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97H TRP* 3.5 42.4 - + - -
352H PHE* 3.4 36.3 - + + -
374H PHE* 3.9 8.7 - + - -
376H MET* 3.7 23.6 - - + -
397H ILE* 4.1 7.6 - - + -
408H GLY 3.5 10.1 - - - +
410H PHE* 3.4 9.4 - - - -
421H CYS* 1.3 77.5 - - - +
423H TRP* 1.3 70.0 + - - +
424H VAL* 3.8 18.2 - - + -
445H SER* 3.2 2.6 - - - -
446H PHE* 2.8 67.1 + + + +
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Residues in contact with TRP 423 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119H GLU 5.6 0.2 - - - -
120H PRO* 3.3 26.7 - - + -
121H PHE* 3.5 20.9 - - + +
122H ILE* 3.6 29.7 + - + +
227H GLU 3.9 1.8 - - - -
228H SER* 4.3 2.5 - - - -
350H LYS* 3.8 20.4 - - + -
406H TYR* 3.4 18.2 - + + -
407H SER* 3.2 36.9 - - - -
408H GLY* 3.1 38.0 + - - +
409H SER 3.9 7.5 + - - -
410H PHE* 3.9 13.2 - + - -
422H PHE* 1.3 76.5 - - - +
424H VAL* 1.3 75.8 + - - +
425H GLU* 3.8 9.6 - - + -
443H SER* 5.6 4.5 - - - -
444H ILE 3.3 12.8 - - - +
445H SER* 4.2 7.9 - - - -
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Residues in contact with VAL 424 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374H PHE* 3.8 38.6 - - + -
397H ILE* 4.6 0.2 - - + -
398H VAL* 5.1 0.2 - - + -
404H SER* 4.5 7.0 - - - -
405H GLY 4.7 0.7 - - - +
406H TYR 3.5 7.9 - - - +
407H SER* 4.2 0.2 - - - -
422H PHE* 3.8 23.1 - - + -
423H TRP* 1.3 84.1 - - - +
425H GLU* 1.3 68.1 + - - +
426H LEU* 3.7 21.9 + - + -
443H SER* 3.2 8.3 - - - -
444H ILE* 2.9 48.9 + - + +
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Residues in contact with GLU 425 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H ARG* 2.4 38.0 + - - -
119H GLU 3.0 17.1 + - - -
120H PRO* 3.4 17.7 - - + +
404H SER 3.1 22.7 - - - +
405H GLY* 3.2 4.3 + - - -
406H TYR* 2.5 54.5 + - + +
423H TRP* 3.7 8.6 - - + -
424H VAL* 1.3 73.1 - - - +
426H LEU* 1.3 62.8 + - - +
427H ILE* 3.1 20.4 - - + +
441H GLY* 4.8 4.9 - - - -
442H SER 3.5 7.4 - - - +
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Residues in contact with LEU 426 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102H LYS* 5.1 1.1 - - - +
106H ILE* 4.3 2.9 - - - +
398H VAL* 4.5 8.7 - - + -
403H TRP 3.8 18.4 - - - +
404H SER* 3.9 5.8 - - - -
424H VAL* 3.7 31.0 - - + +
425H GLU* 1.3 72.0 - - - +
427H ILE* 1.3 59.9 + - - +
428H ARG* 3.8 3.9 + - - +
441H GLY* 3.1 4.2 - - - -
442H SER* 2.8 46.7 + - - +
443H SER 4.6 0.7 - - - +
444H ILE* 4.2 21.5 - - + -
458H TRP 3.8 8.7 - - - +
459H PRO 3.5 7.4 - - - +
460H ASP* 3.2 45.1 - - + +
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Residues in contact with ILE 427 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H ARG* 3.7 22.7 - - - +
371H ARG* 4.0 18.8 - - + +
403H TRP* 3.4 17.3 + - - +
404H SER* 3.0 14.8 + - - +
405H GLY* 4.0 12.8 - - - -
425H GLU* 3.1 37.2 - - + +
426H LEU* 1.3 70.5 - - - +
428H ARG* 1.3 74.6 + - - +
429H GLY 5.8 0.2 - - - +
430H ARG 4.8 6.1 - - - +
431H PRO* 6.2 0.7 - - + -
433H GLU* 4.4 0.7 - - - +
439H THR* 4.2 18.6 - - + -
440H SER 3.5 11.9 - - - +
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Residues in contact with ARG 428 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ILE* 3.8 17.5 - - + -
403H TRP* 3.5 22.2 - - - -
426H LEU 3.8 0.9 + - - +
427H ILE* 1.3 88.0 - - - +
429H GLY* 1.3 60.1 + - - +
433H GLU* 2.8 32.1 + - - +
438H TRP* 3.7 10.3 - - + -
439H THR* 3.5 3.6 - - - +
440H SER 3.0 30.5 + - - +
460H ASP* 3.0 48.2 + - + +
461H GLY 4.3 2.2 - - - +
462H ALA* 2.8 30.9 + - - +
463H GLU* 4.8 0.4 - - - +
464H LEU* 3.5 23.2 - - + +
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Residues in contact with GLY 429 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427H ILE* 5.8 0.3 - - - +
428H ARG* 1.3 74.6 - - - +
430H ARG* 1.3 62.7 + - - +
432H LYS* 3.5 4.0 + - - +
433H GLU* 2.7 47.4 + - - +
436H THR* 3.3 10.5 - - - -
438H TRP* 3.2 13.7 - - - -
464H LEU* 3.7 6.0 - - - +
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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