Contacts of the helix formed by residues 96 - 104 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU 3.5 16.8 - - - +
93A LEU* 2.7 19.5 + - - +
94A LEU 3.1 0.4 + - - -
95A ALA* 1.3 78.4 - - + +
97A LEU* 1.3 63.2 + - - +
98A PRO* 3.4 1.1 - - - -
99A LEU* 3.2 18.5 + - + +
100A TRP* 3.0 37.4 + - + -
120A PHE* 4.8 7.9 - - + +
123A PHE* 4.1 20.6 - - + -
124A LEU* 3.4 19.2 - - + +
308A PHE* 3.9 0.9 - - - -
162B TYR* 3.4 11.9 - - - +
166B LEU* 6.1 0.4 - - + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 3.6 48.0 - - + +
52A TYR* 6.0 0.4 - - - -
54A ILE* 3.9 10.5 - - + -
55A PHE* 3.8 17.7 - - + -
94A LEU* 3.0 46.2 + - + +
96A THR* 1.3 76.5 + - - +
98A PRO* 1.4 64.0 - - + +
100A TRP* 3.3 7.3 + - + +
101A ALA* 3.0 24.9 + - - +
305A LEU* 4.6 3.6 - - + -
308A PHE* 3.8 36.8 - - + -
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Residues in contact with PRO 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 3.6 37.7 + - + +
55A PHE* 4.2 22.9 - - + -
94A LEU 4.0 2.2 - - - +
95A ALA 3.3 18.8 - - - +
96A THR 3.5 1.1 - - - -
97A LEU* 1.4 90.9 - - + +
99A LEU* 1.4 56.5 + - - +
101A ALA 3.6 0.7 + - - -
102A THR* 2.7 34.2 + - - -
162B TYR* 4.3 17.9 - - + -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A THR* 3.2 15.5 + - - +
98A PRO* 1.4 76.2 - - - +
100A TRP* 1.3 73.0 + - + +
102A THR* 3.5 2.8 + - - -
103A TYR* 3.0 28.8 + - - +
110A TRP* 4.8 4.2 - - + -
112A PHE* 3.6 45.2 - - + -
116A MET* 4.6 5.6 - - + -
120A PHE* 3.6 33.9 - - + -
162B TYR* 3.3 46.7 - - + +
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Residues in contact with TRP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A TYR* 4.3 7.6 - - + -
96A THR* 3.0 43.4 + - - -
97A LEU* 3.3 7.3 + - + +
99A LEU* 1.3 81.0 - - + +
101A ALA* 1.3 61.5 + - - +
102A THR 3.2 1.6 - - - -
103A TYR* 4.3 5.2 - + - -
104A TYR* 3.1 24.6 + - - +
110A TRP* 3.8 28.5 - + - -
120A PHE* 4.0 31.9 - - + -
124A LEU* 3.4 27.6 - - + +
308A PHE* 4.0 12.6 - + - -
1501A 8EM 3.2 86.0 - + + -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ILE* 6.2 0.2 - - - -
48A PRO* 3.7 18.8 - - + +
51A TYR* 3.7 26.6 - - + -
52A TYR* 3.6 30.4 - - + -
97A LEU 3.0 16.1 + - - +
98A PRO 4.1 0.7 - - - +
100A TRP* 1.3 75.3 - - - +
102A THR* 1.4 53.4 + - - +
104A TYR* 4.3 2.9 - - - +
105A SER* 2.7 31.5 + - - -
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Residues in contact with THR 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A TYR* 4.0 10.4 + - - -
98A PRO* 2.7 22.8 + - - +
99A LEU 3.7 4.0 - - - -
101A ALA* 1.4 76.2 - - - +
103A TYR* 1.4 64.8 + - - +
104A TYR 3.3 0.2 - - - -
105A SER* 3.1 14.1 + - - -
106A TYR* 3.2 46.2 + - + -
112A PHE* 4.1 21.9 - - + -
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Residues in contact with TYR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU 3.0 18.1 + - - +
100A TRP* 4.1 7.4 - + - +
102A THR* 1.4 74.0 - - - +
104A TYR* 1.4 60.0 + - - +
106A TYR* 3.2 9.2 + - - -
108A TYR* 3.1 66.3 + + + +
109A ASP 3.9 5.8 + - - -
110A TRP* 3.5 46.7 - + + -
112A PHE* 4.9 4.2 - - + -
194A ALA* 3.4 10.9 - - - +
195A CYS* 3.0 38.9 + - + -
196A ILE* 4.5 1.9 - - - +
1501A 8EM 3.0 43.5 - + - -
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Residues in contact with TYR 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LYS 3.9 5.5 + - - -
43A HIS* 3.4 33.2 - + - -
44A LEU* 2.9 43.8 + - - +
47A ILE* 3.2 39.7 - - + +
48A PRO* 3.7 18.8 - - + -
100A TRP 3.1 19.8 + - - +
101A ALA* 4.3 4.7 - - - +
103A TYR* 1.4 75.9 - - - +
105A SER* 1.4 57.1 + - - +
107A ARG* 3.5 12.4 + - - -
108A TYR* 3.3 40.5 + + - +
301A PRO* 4.4 9.0 - - + -
1501A 8EM 3.8 15.0 - + + -
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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