Contacts of the strand formed by residues 439 - 447 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116E VAL* 3.3 15.6 - - - +
117E ILE 3.8 2.8 - - - +
118E ARG* 4.2 22.9 - - + +
136E GLN* 5.3 0.5 - - - +
148E THR* 3.1 24.2 + - - +
149E VAL* 3.3 21.3 - - + +
427E ILE* 4.2 17.0 - - + -
428E ARG 3.5 5.8 - - - -
430E ARG 2.8 35.4 + - - +
438E TRP* 1.3 73.7 + - - +
440E SER* 1.3 67.3 + - - +
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Residues in contact with SER 440 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106E ILE* 3.7 8.7 - - - +
115E PHE 4.1 2.3 + - - -
116E VAL* 3.5 10.7 - - - -
117E ILE* 2.7 37.2 + - - +
118E ARG* 4.5 4.3 - - - -
140E LEU* 3.9 21.8 - - - +
427E ILE* 3.5 4.1 - - - +
428E ARG 2.8 32.7 + - - +
438E TRP* 3.8 6.0 - - - -
439E THR* 1.3 77.8 - - - +
441E GLY* 1.3 64.5 + - - +
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Residues in contact with GLY 441 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E SER* 3.3 11.8 + - - -
106E ILE* 4.1 5.9 - - - +
117E ILE* 3.4 31.0 + - - +
118E ARG* 4.7 0.4 - - - +
120E PRO* 5.8 0.4 - - - -
425E GLU* 4.5 11.4 - - - -
426E LEU 3.3 13.0 - - - -
427E ILE* 4.3 1.8 - - - -
440E SER* 1.3 84.2 + - - +
442E SER* 1.3 61.7 + - - -
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Residues in contact with SER 442 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102E LYS* 6.0 0.9 - - - -
103E ASP* 3.6 3.5 + - - -
104E ASN* 4.0 4.0 - - - -
105E SER* 2.8 32.3 + - - -
106E ILE* 3.5 2.6 + - - +
117E ILE* 5.9 0.7 - - - -
120E PRO* 4.4 3.3 - - - +
425E GLU* 3.2 9.9 - - - +
426E LEU* 2.9 40.2 + - - -
441E GLY* 1.3 73.2 - - - -
443E SER* 1.3 64.6 - - - +
460E ASP* 3.0 28.3 + - - -
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Residues in contact with SER 443 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E SER* 4.7 2.6 + - - -
102E LYS* 3.4 4.3 - - - +
103E ASP* 2.5 50.6 + - - +
104E ASN 4.9 0.2 + - - -
120E PRO* 4.7 17.0 - - - -
122E ILE* 5.7 5.8 - - - +
131E THR* 4.8 10.4 + - - +
423E TRP* 5.6 5.6 - - - -
424E VAL 3.1 11.7 - - - -
426E LEU* 4.7 0.9 - - - -
442E SER* 1.3 81.2 - - - +
444E ILE* 1.3 69.0 + - - +
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Residues in contact with ILE 444 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E VAL* 5.9 1.6 - - + -
101E SER* 3.3 9.6 - - - +
102E LYS* 3.9 21.5 - - + -
122E ILE* 5.5 0.2 - - - -
397E ILE* 3.7 17.3 - - + -
398E VAL* 3.7 23.3 - - + -
423E TRP* 3.4 2.6 - - - +
424E VAL* 3.0 45.7 + - + +
426E LEU* 4.0 14.8 - - + -
443E SER* 1.3 81.0 - - - +
445E SER* 1.3 62.8 + - - +
446E PHE* 4.0 13.5 - - + -
458E TRP* 3.4 33.9 - - + +
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Residues in contact with SER 445 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E VAL* 3.6 2.3 - - - +
100E TYR* 2.6 39.9 + - - +
101E SER* 2.6 38.1 + - - +
122E ILE* 3.4 25.5 - - - +
410E PHE* 4.3 6.1 - - - -
422E PHE 3.4 11.4 - - - -
423E TRP* 4.1 0.4 - - - -
444E ILE* 1.3 76.5 - - - +
446E PHE* 1.3 65.4 + - - +
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Residues in contact with PHE 446 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E TRP* 3.9 18.2 - - + -
98E ALA 3.0 11.4 - - - +
99E VAL* 3.5 33.4 - - + -
100E TYR* 3.9 2.7 - - - +
395E GLN* 5.4 1.1 - - - -
397E ILE* 3.8 32.5 - - + -
410E PHE* 4.2 0.5 - - - -
421E CYS* 3.0 5.9 - - - +
422E PHE* 2.9 62.7 + + + -
444E ILE* 4.0 21.1 - - + -
445E SER* 1.3 81.2 - - - +
447E CYS* 1.3 64.5 + - - +
458E TRP* 3.6 40.8 - + - -
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Residues in contact with CYS 447 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97E TRP* 3.6 7.0 - - - -
98E ALA* 2.9 25.4 + - - +
100E TYR* 4.1 18.4 - - - +
410E PHE* 4.3 0.9 - - - -
412E GLN* 2.6 20.6 - - - -
419E ARG* 4.1 11.2 - - - +
420E PRO 3.8 0.7 - - - -
421E CYS* 2.1 44.0 - - - +
446E PHE* 1.3 75.2 - - - +
448E GLY* 1.3 70.4 + - - +
449E VAL* 4.0 3.4 - - + +
211G ILE* 3.9 17.9 - - + -
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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