Contacts of the strand formed by residues 419 - 429 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210B ILE* 4.7 3.2 - - - +
211B ILE* 2.9 46.2 + - - +
212B THR* 5.2 1.8 - - - +
92C CYS* 3.8 14.5 - - + +
411C VAL* 3.5 7.2 - - - +
412C GLN* 2.7 76.2 + - + +
413C THR* 5.0 4.9 - - - +
415C LEU* 4.1 27.3 - - + +
417C CYS 3.5 2.4 + - - -
418C ILE* 1.3 73.0 - - - +
420C PRO* 1.3 76.7 - - + +
421C CYS* 3.9 6.5 + - - -
447C CYS* 4.3 8.4 - - - +
448C GLY* 4.4 2.7 - - - +
449C VAL* 4.4 26.0 - - - +
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Residues in contact with PRO 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU* 4.7 6.1 - - + -
92C CYS* 4.1 10.3 - - + +
94C ILE* 4.3 21.5 - - + -
97C TRP* 3.4 5.4 - - + -
354C PHE* 3.4 39.9 - - + -
356C TYR* 3.4 24.9 - - - +
410C PHE 4.4 1.1 - - - +
411C VAL* 5.0 1.3 - - + -
418C ILE 3.5 8.5 - - - +
419C ARG* 1.3 86.6 - - + +
421C CYS* 1.3 55.0 + - - +
448C GLY* 2.6 33.6 + - - -
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Residues in contact with CYS 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C TRP* 4.2 2.0 - - - -
354C PHE* 3.3 11.0 - - - -
410C PHE* 3.0 46.9 + - + +
412C GLN* 2.7 30.1 - - - -
419C ARG* 4.0 2.9 - - - -
420C PRO* 1.3 75.0 - - - +
422C PHE* 1.3 63.6 + - - +
446C PHE 2.9 15.7 - - - +
447C CYS* 2.1 44.9 - - - +
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Residues in contact with PHE 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C TRP* 3.6 35.0 - + - -
352C PHE* 3.3 35.2 - + + -
374C PHE* 3.7 12.6 - + - -
376C MET* 3.7 23.6 - - + -
397C ILE* 4.1 7.2 - - + -
408C GLY 3.2 15.3 - - - +
410C PHE* 3.6 6.3 - - - -
421C CYS* 1.3 76.2 - - - +
423C TRP* 1.3 63.1 + - - +
424C VAL* 3.6 26.5 - - + -
445C SER* 3.1 4.5 - - - -
446C PHE* 2.8 70.6 + + + +
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Residues in contact with TRP 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C PRO* 3.0 30.7 - - + -
121C PHE* 3.4 20.6 - - + +
122C ILE* 3.3 42.0 + - + +
227C GLU 3.8 10.8 - - - -
228C SER* 4.2 3.1 - - - -
350C LYS* 4.0 10.1 - - + -
406C TYR* 3.6 17.0 - + + -
407C SER* 3.2 28.7 - - - -
408C GLY* 3.0 48.9 + - - -
409C SER 4.4 4.6 + - - -
410C PHE* 3.7 14.1 - + + -
422C PHE* 1.3 75.7 - - - +
424C VAL* 1.3 67.9 + - - +
425C GLU* 3.7 14.6 - - + -
443C SER* 5.6 4.9 - - - -
444C ILE 3.3 10.3 - - - +
445C SER* 4.0 0.2 - - - +
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Residues in contact with VAL 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C PHE* 3.8 39.5 - - + -
397C ILE* 4.5 0.2 - - + -
404C SER* 4.5 7.0 - - - -
405C GLY 4.8 0.2 - - - +
406C TYR 3.5 9.2 - - - +
422C PHE* 3.6 25.8 - - + -
423C TRP* 1.3 82.7 - - - +
425C GLU* 1.3 70.9 + - - +
426C LEU* 3.8 12.5 + - + +
443C SER* 3.4 6.5 - - - -
444C ILE* 2.7 55.4 + - + +
446C PHE* 5.0 0.2 - - + -
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Residues in contact with GLU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ARG* 2.7 35.7 + - - -
119C GLU 2.8 19.8 + - - -
120C PRO* 3.1 29.1 - - + +
404C SER* 3.0 2.9 - - - -
405C GLY* 3.0 27.2 + - - -
406C TYR* 2.6 46.5 + - + +
423C TRP* 3.7 3.6 - - + -
424C VAL* 1.3 72.2 - - - +
426C LEU* 1.3 63.5 + - - +
427C ILE* 3.3 20.5 - - + +
441C GLY* 4.9 5.3 - - - -
442C SER 3.6 5.2 - - - +
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Residues in contact with LEU 426 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LYS* 5.1 1.3 - - - +
106C ILE* 4.1 4.9 - - - +
398C VAL* 4.3 15.9 - - + -
403C TRP 3.5 20.2 - - - +
404C SER* 3.8 11.4 - - - +
424C VAL* 4.2 17.7 - - + +
425C GLU* 1.3 72.4 - - - +
427C ILE* 1.3 62.1 + - - +
428C ARG* 3.6 3.9 + - - +
441C GLY* 3.2 4.6 - - - -
442C SER* 2.7 46.6 + - - +
443C SER 5.0 0.2 - - - +
444C ILE* 4.0 17.5 - - + -
458C TRP 3.8 8.1 - - - +
459C PRO* 3.6 8.7 - - + +
460C ASP* 3.5 37.5 - - + +
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Residues in contact with ILE 427 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ARG* 3.8 22.9 - - - +
371C ARG* 4.2 18.8 - - + +
403C TRP* 3.3 27.0 - - - +
404C SER 3.0 13.9 + - - +
405C GLY* 3.6 18.2 - - - -
406C TYR 4.3 0.4 - - - +
425C GLU* 3.3 35.7 - - + +
426C LEU* 1.3 71.1 - - - +
428C ARG* 1.3 64.8 + - - +
429C GLY 5.7 0.2 - - - +
430C ARG 4.7 5.8 - - - +
431C PRO* 6.1 1.1 - - + -
433C GLU* 4.3 0.3 - - - +
439C THR* 4.1 21.1 - - + -
440C SER 3.6 10.3 - - - +
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Residues in contact with ARG 428 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ILE* 3.5 18.4 - - + -
403C TRP* 3.5 20.8 - - - -
426C LEU 4.1 1.6 - - - +
427C ILE* 1.3 88.6 - - - +
429C GLY* 1.3 60.1 + - - +
433C GLU* 2.7 37.9 + - - +
438C TRP* 3.6 7.9 - - + -
439C THR* 3.6 2.9 - - - -
440C SER 2.9 31.2 + - - +
460C ASP* 2.9 49.6 + - + +
461C GLY 4.3 2.0 - - - +
462C ALA* 2.7 33.3 + - - +
463C GLU* 4.9 0.2 - - - +
464C LEU* 3.5 22.3 - - + +
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Residues in contact with GLY 429 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427C ILE* 5.7 0.3 - - - +
428C ARG* 1.3 74.3 - - - +
430C ARG* 1.3 66.9 + - - +
432C LYS* 3.2 4.5 + - - +
433C GLU* 2.8 41.7 + - - +
436C THR* 3.3 19.3 - - - -
438C TRP* 3.3 6.7 - - - -
464C LEU* 3.6 5.4 - - - +
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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