Contacts of the strand formed by residues 439 - 447 (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 THR 439 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116H VAL* 3.2 21.5 - - - +
117H ILE 4.0 1.4 - - - +
118H ARG* 4.1 27.9 - - + +
136H GLN* 5.2 0.3 - - - +
148H THR* 3.2 26.0 + - - +
149H VAL* 3.2 20.6 - - + +
427H ILE* 4.2 7.4 - - + -
428H ARG 3.5 9.4 - - - +
430H ARG 2.7 29.6 + - - +
438H TRP* 1.3 79.9 + - - +
440H SER* 1.3 63.8 + - - +
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Residues in contact with SER 440 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H ILE* 4.2 8.0 - - - +
115H PHE 4.2 2.1 + - - -
116H VAL* 3.5 4.8 - - - -
117H ILE* 2.9 32.9 + - - +
118H ARG* 4.3 4.3 - - - -
140H LEU* 3.8 26.2 - - - +
427H ILE* 3.5 7.4 - - - +
428H ARG 3.0 29.2 + - - +
438H TRP* 3.8 7.8 - - - -
439H THR* 1.3 78.0 - - - +
441H GLY* 1.3 69.2 + - - +
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Residues in contact with GLY 441 (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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105H SER* 3.6 7.3 + - - -
106H ILE* 3.9 8.3 - - - +
117H ILE* 3.3 32.3 + - - +
118H ARG* 5.0 2.2 - - - -
120H PRO* 5.7 1.1 - - - -
425H GLU* 4.8 8.5 - - - -
426H LEU 3.1 12.6 - - - -
427H ILE* 4.3 1.6 - - - -
440H SER* 1.3 84.9 + - - +
442H SER* 1.3 63.0 + - - -
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Residues in contact with SER 442 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102H LYS* 5.5 1.2 + - - -
103H ASP* 3.2 10.4 + - - -
104H ASN* 3.8 6.1 + - - -
105H SER* 3.0 28.8 + - - -
106H ILE* 3.7 3.3 + - - +
117H ILE* 5.9 0.7 - - - -
120H PRO* 4.5 2.4 - - - +
425H GLU* 3.5 6.1 - - - +
426H LEU* 2.8 38.0 + - - -
441H GLY* 1.3 75.9 - - - -
443H SER* 1.3 64.7 + - - +
460H ASP* 3.2 29.6 + - - -
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Residues in contact with SER 443 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H SER* 5.4 2.2 + - - -
102H LYS* 3.6 1.6 - - - +
103H ASP* 2.7 54.1 + - - +
120H PRO* 4.6 16.4 - - - -
122H ILE* 5.8 5.1 - - - +
131H THR* 4.8 11.8 + - - +
423H TRP* 5.6 5.2 - - - -
424H VAL 3.2 13.2 - - - -
426H LEU* 4.6 3.1 - - - +
442H SER* 1.3 80.2 + - - +
444H ILE* 1.3 70.4 + - - +
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Residues in contact with ILE 444 (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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99H VAL* 6.1 0.9 - - + -
101H SER* 3.2 11.2 - - - +
102H LYS* 3.5 26.7 - - + -
122H ILE* 5.7 0.4 - - - -
397H ILE* 3.7 18.8 - - + -
398H VAL* 3.9 13.9 - - + -
423H TRP* 3.3 5.0 - - - +
424H VAL* 2.9 49.7 + - + +
426H LEU* 4.2 9.6 - - + -
443H SER* 1.3 81.2 - - - +
445H SER* 1.3 62.5 + - - +
446H PHE* 3.7 26.5 - - + -
458H TRP* 3.8 23.6 - - + +
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Residues in contact with SER 445 (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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99H VAL* 3.7 1.0 - - - +
100H TYR* 2.7 48.9 + - - +
101H SER* 2.8 29.2 + - - +
122H ILE* 3.6 24.9 - - - +
410H PHE* 3.9 5.2 - - - -
422H PHE 3.2 12.1 - - - -
423H TRP* 4.2 0.7 - - - -
444H ILE* 1.3 77.7 - - - +
446H PHE* 1.3 67.7 + - - +
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Residues in contact with PHE 446 (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* 4.1 13.7 - - + -
98H ALA* 3.2 11.7 - - - +
99H VAL* 3.5 43.7 - - + -
100H TYR* 4.0 1.8 - - - -
395H GLN* 5.8 0.7 - - - -
397H ILE* 3.8 20.0 - - + -
410H PHE* 4.1 0.5 - - - -
421H CYS* 2.9 6.8 - - - +
422H PHE* 2.8 69.5 + + + +
444H ILE* 3.7 30.3 - - + -
445H SER* 1.3 80.1 - - - +
447H CYS* 1.3 65.6 + - - +
458H TRP* 3.8 35.2 - + - -
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Residues in contact with CYS 447 (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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211E ILE* 4.1 17.0 - - + -
97H TRP* 3.5 8.8 - - - -
98H ALA* 3.1 24.7 + - - -
100H TYR* 4.1 17.5 - - - -
410H PHE* 4.1 2.2 - - - -
412H GLN* 2.6 20.4 - - - +
419H ARG* 4.2 9.6 - - - +
420H PRO 3.8 0.2 - - - -
421H CYS* 2.1 45.8 - - - +
446H PHE* 1.3 75.8 - - - +
448H GLY* 1.3 70.3 + - - +
449H VAL* 3.9 3.6 - - + +
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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