Contacts of the helix formed by residues 84 - 90 (chain D) in PDB entry 5UHA
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 84 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D PRO* 3.7 1.8 - - - +
57D ASP* 3.7 24.9 - - - +
58D TRP* 3.5 37.1 - - + +
83D THR* 1.3 102.9 - - + +
85D ALA* 1.3 61.8 + - - +
86D LYS* 2.9 27.4 + - + +
87D VAL* 3.4 21.5 + - + +
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Residues in contact with ALA 85 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D PRO* 3.2 16.9 + - - +
55D THR 3.2 28.0 - - - +
56D ARG* 4.5 0.4 - - - +
57D ASP* 3.1 17.7 + - - +
84D ARG* 1.3 70.3 - - - +
86D LYS* 1.3 53.5 + - - +
87D VAL 2.9 6.3 - - - -
88D ARG* 2.8 37.5 + - - +
89D ARG* 4.8 2.4 - - - +
323D GLU* 4.9 3.1 - - - +
443F GLU* 5.3 11.8 - - + +
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Residues in contact with LYS 86 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1054C GLN* 4.7 8.5 - - - +
1096C THR* 3.7 35.9 + - - +
1119C GLU* 4.2 1.7 + - - -
1148C ARG* 2.4 59.4 + - - +
57D ASP* 4.7 0.4 + - - -
84D ARG* 3.5 24.2 - - + +
85D ALA* 1.3 75.5 - - - +
87D VAL* 1.3 57.5 + - + +
88D ARG 3.3 0.2 - - - -
89D ARG* 3.7 38.9 + - - +
443F GLU* 4.6 14.9 + - - +
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Residues in contact with VAL 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1148C ARG* 5.5 0.2 - - - +
52D PHE 3.2 17.5 - - - +
53D GLY* 3.8 13.5 - - - -
54D PRO* 4.0 3.6 - - + -
83D THR* 4.3 17.9 - - + -
84D ARG* 3.5 20.2 - - + +
85D ALA 2.9 1.6 + - - -
86D LYS* 1.3 76.4 - - + +
88D ARG* 1.3 59.2 + - - +
89D ARG 2.9 5.8 - - - -
90D GLU* 2.8 38.2 + - - +
91D ARG* 3.0 48.1 + - + +
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D PRO* 4.9 3.8 - - - +
47D PHE* 3.3 55.2 + - - +
49D GLU* 4.0 6.7 - - - +
52D PHE* 3.6 24.2 - - + +
53D GLY* 3.1 24.7 + - - +
54D PRO 3.6 21.5 - - - +
55D THR* 4.4 11.2 - - - +
85D ALA* 2.8 18.0 + - - +
87D VAL* 1.3 76.4 - - + +
89D ARG* 1.3 59.0 + - - +
90D GLU 3.5 0.2 - - - -
321D PRO* 3.6 2.4 - - - +
322D PRO* 3.3 26.8 - - + +
323D GLU* 3.1 44.0 + - + -
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Residues in contact with ARG 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051C MET 3.9 9.3 + - - -
1052C ILE* 2.4 34.6 + - - +
1054C GLN* 3.4 23.7 - - - +
1119C GLU* 2.4 41.9 + - - +
1123C VAL* 4.5 8.8 - - - +
1126C LYS* 4.3 5.9 - - - +
1148C ARG* 4.8 3.8 + - - +
85D ALA 4.8 1.3 - - - +
86D LYS* 3.9 36.3 - - - +
87D VAL 2.9 1.2 - - - -
88D ARG* 1.3 78.8 - - - +
90D GLU* 1.3 58.9 + - - +
91D ARG 3.8 0.2 - - - -
321D PRO* 3.9 8.7 - - - +
323D GLU* 3.5 31.0 + - + +
324D LEU* 3.8 28.1 - - + +
443F GLU* 5.0 8.2 + - - -
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Residues in contact with GLU 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1126C LYS* 3.4 32.4 + - + +
1147C LEU 5.7 0.2 - - - +
1148C ARG* 2.8 58.9 + - - +
1149C GLU* 3.3 23.9 - - + +
1150C GLY 5.2 2.1 + - - +
25D TYR* 4.9 1.7 + - - -
87D VAL* 2.8 33.4 + - - +
89D ARG* 1.3 82.2 - - - +
91D ARG* 1.3 70.7 + - + +
92D MET 3.8 0.7 + - - -
321D PRO* 4.2 4.7 - - - -
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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