Contacts of the helix formed by residues 96 - 106 (chain B) in PDB entry 5UNH
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 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B LEU 3.6 15.0 - - - +
93B LEU* 2.7 19.7 + - - -
94B LEU 3.1 0.2 + - - -
95B ALA* 1.3 76.8 - - + +
97B LEU* 1.4 63.5 + - - +
98B PRO* 3.5 1.1 - - - -
99B LEU* 3.2 27.0 + - + +
100B TRP* 3.2 39.5 + - + -
120B PHE* 5.1 7.4 - - + +
123B PHE* 4.0 22.9 - - + -
124B LEU* 3.5 15.3 - - + +
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 3.6 49.0 - - + +
52B TYR* 5.8 0.7 - - - -
54B ILE* 3.9 14.6 - - + -
55B PHE* 3.8 18.2 - - + -
93B LEU 4.8 2.5 - - - +
94B LEU* 3.0 49.3 + - + +
96B THR* 1.4 76.5 + - - +
98B PRO* 1.4 65.3 - - + +
99B LEU 3.2 0.3 + - - -
100B TRP* 3.2 12.1 + - + +
101B ALA* 3.1 22.7 + - - +
305B LEU* 4.6 2.9 - - + -
308B PHE* 4.3 15.7 - - + -
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Residues in contact with PRO 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B TYR* 6.6 0.2 - - - -
55B PHE* 4.2 26.7 - - + -
94B LEU 4.0 2.0 - - - +
95B ALA 3.3 19.7 - - - +
96B THR 3.5 1.1 - - - -
97B LEU* 1.4 92.4 - - + +
99B LEU* 1.3 56.4 + - + +
101B ALA* 3.6 7.9 - - + +
102B THR* 2.7 38.9 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ALA 4.3 13.9 - - - +
96B THR* 3.2 19.9 + - + +
97B LEU 3.2 0.4 - - - -
98B PRO* 1.3 84.0 - - + +
100B TRP* 1.4 71.8 + - + +
102B THR* 3.8 4.8 - - - -
103B TYR* 3.0 27.5 + - - +
112B PHE* 6.3 3.8 - - + -
116B MET* 6.4 1.3 - - + -
120B PHE* 4.2 25.1 - - + -
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Residues in contact with TRP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B TYR* 4.3 10.3 - + + -
96B THR* 3.2 43.3 + - + -
97B LEU* 3.2 15.3 + - + +
99B LEU* 1.4 86.3 - - + +
101B ALA* 1.4 59.4 + - - +
103B TYR* 3.8 13.2 - + + -
104B TYR* 3.1 22.9 + - - +
120B PHE* 4.0 31.4 - - + -
121B GLY 4.7 0.2 - - - -
124B LEU* 3.4 30.0 - - + +
195B CYS* 5.9 1.1 - - - -
1501B 8EM 3.2 91.4 - + + -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 6.4 0.4 - - - -
48B PRO* 4.1 20.8 - - + +
51B TYR* 4.1 23.3 - - + -
52B TYR* 5.3 3.8 - - + +
97B LEU 3.1 16.0 + - - +
98B PRO* 3.6 10.1 - - + +
99B LEU 3.3 0.2 - - - -
100B TRP* 1.4 76.2 - - - +
102B THR* 1.4 53.6 + - - +
104B TYR* 3.5 5.5 + - - +
105B SER* 2.9 35.8 + - - -
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Residues in contact with THR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PRO* 2.7 23.0 + - - +
99B LEU* 3.8 5.6 - - - -
101B ALA* 1.4 72.7 - - - +
103B TYR* 1.4 65.3 + - - +
105B SER* 3.1 16.7 + - - -
106B TYR* 3.2 45.3 - - + -
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU 3.0 18.4 + - - +
100B TRP* 3.7 17.0 - + + +
102B THR* 1.4 77.0 - - - +
104B TYR* 1.3 55.8 + - - +
106B TYR* 3.8 3.7 + - - -
108B TYR* 3.0 58.0 + + - -
109B ASP 3.3 41.6 + - - -
110B TRP* 4.0 6.5 - - + -
194B ALA* 3.6 11.3 - - - +
195B CYS* 3.2 44.9 + - + -
196B ILE* 4.9 1.2 - - - +
1501B 8EM 3.2 42.1 + + - -
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Residues in contact with TYR 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B LEU* 3.5 36.7 + - - +
47B ILE* 3.4 43.1 - - + +
48B PRO* 4.0 11.4 - - + -
100B TRP 3.1 18.8 + - - +
101B ALA* 3.9 5.2 - - - +
103B TYR* 1.3 72.6 - - - +
105B SER* 1.4 59.8 + - - +
106B TYR 3.2 2.0 - - - -
107B ARG* 3.0 20.1 + - - +
108B TYR* 4.0 32.3 - + - +
301B PRO* 4.2 16.6 - - + +
1501B 8EM 4.0 18.4 - + + -
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 3.7 19.1 - - - +
101B ALA 2.9 18.8 + - - -
102B THR* 3.1 14.4 + - - -
104B TYR* 1.4 76.5 - - - +
106B TYR* 1.3 65.7 + - - +
107B ARG* 3.3 1.8 + - - +
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Residues in contact with TYR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B THR* 3.2 44.6 + - + +
103B TYR* 3.8 2.0 + - - +
104B TYR 3.2 0.8 - - - -
105B SER* 1.3 81.7 - - - +
107B ARG* 1.4 61.4 + - - +
108B TYR 3.6 1.6 - - - -
109B ASP* 2.9 49.6 - - + +
111B LEU* 4.6 23.8 - - + -
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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