Contacts of the helix formed by residues 103 - 109 (chain A) in PDB entry 5HVO
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 ILE 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A GLY 3.8 17.5 - - - +
99A PHE* 2.9 32.1 + - + +
102A SER* 1.3 86.6 - - - +
104A LEU* 1.3 65.2 + - - +
105A TRP 3.5 0.7 - - - -
106A PRO* 3.2 13.1 - - - +
107A LEU* 3.3 14.9 + - - +
113A GLY 5.6 1.8 - - - -
114A GLU* 5.1 13.0 - - + -
117A PHE* 4.2 19.5 - - + -
118A ASP* 4.1 30.7 - - + +
121A ALA* 4.7 0.2 - - + -
191A LEU* 3.7 26.9 - - + -
192A PRO* 5.7 0.2 - - + -
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Residues in contact with LEU 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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99A PHE* 2.9 35.0 + - + +
100A SER* 3.3 11.0 - - - +
103A ILE* 1.3 72.1 - - - +
105A TRP* 1.3 67.7 + - - +
107A LEU* 3.2 5.9 + - + +
108A LEU* 2.9 43.6 + - + +
125A TYR* 3.9 11.2 - - + +
151A TYR* 3.3 34.8 - - + +
154A MET* 3.5 26.7 - - + -
188A TYR* 5.7 1.1 - - + -
191A LEU* 4.6 9.0 - - + -
197A LEU* 4.1 15.5 - - + -
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Residues in contact with TRP 105 (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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100A SER 2.7 21.0 + - - +
101A ASN* 3.9 10.3 - - - +
104A LEU* 1.3 75.7 - - - +
106A PRO* 1.4 66.1 - - + +
108A LEU* 3.4 3.1 + - - -
109A HIS* 2.7 55.5 + + - -
151A TYR* 3.5 32.3 - + + -
180A THR* 3.7 14.4 - - + -
287A ARG* 3.3 31.0 - - - -
289A ASP* 3.2 12.3 + - - -
290A TYR* 3.2 22.4 - + - -
291A ILE* 3.4 24.5 - - + +
325A ARG* 3.1 13.2 - - - +
331A TYR* 3.0 21.8 + + - -
502A VDM 3.6 25.6 - - - -
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Residues in contact with PRO 106 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ASN 3.6 10.5 - - - +
102A SER 3.1 21.8 - - - +
103A ILE* 3.2 17.9 - - - +
105A TRP* 1.4 94.3 - - + +
107A LEU* 1.3 61.5 + - - +
109A HIS* 3.0 6.8 + - + -
111A HIS* 2.9 49.9 + - + +
113A GLY* 4.7 12.6 - - - +
290A TYR* 3.3 24.9 - - + +
330A GLU* 6.3 0.7 - - + -
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Residues in contact with LEU 107 (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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103A ILE 3.3 16.8 + - - +
104A LEU* 3.2 9.5 + - + +
106A PRO* 1.3 79.3 - - - +
108A LEU* 1.3 63.7 + - + +
109A HIS 3.1 1.0 + - - -
110A TYR 3.2 9.9 + - - +
111A HIS 3.9 5.8 + - - +
112A PRO* 5.9 3.1 - - + -
183A PRO* 3.9 1.8 - - + +
187A ILE* 3.5 43.4 - - + +
188A TYR* 4.0 21.3 - - + +
190A ILE* 3.9 25.4 - - + -
191A LEU* 3.6 42.0 - - + +
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Residues in contact with LEU 108 (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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104A LEU* 2.9 38.6 + - + +
105A TRP* 4.0 4.5 - - - +
106A PRO 3.3 0.2 - - - -
107A LEU* 1.3 75.7 - - + +
109A HIS* 1.3 63.7 + - - +
110A TYR* 3.4 3.0 + - - -
151A TYR* 3.8 28.9 - - + -
154A MET* 4.0 7.6 - - + -
178A LEU* 4.5 1.8 - - + -
180A THR* 3.4 23.3 - - + +
181A PRO* 3.8 30.9 - - - +
182A PHE* 4.5 13.7 - - + -
183A PRO* 3.6 35.6 - - + +
188A TYR* 4.7 8.5 - - + -
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Residues in contact with HIS 109 (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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105A TRP* 2.7 70.4 + + - +
106A PRO* 3.0 6.1 + - + +
108A LEU* 1.3 80.4 - - + +
110A TYR* 1.3 72.8 + - - +
111A HIS* 3.1 8.1 + - + +
180A THR* 3.8 16.2 - - + -
181A PRO* 3.2 28.5 - - + +
291A ILE* 3.6 38.7 - - + +
384A THR* 5.5 0.9 + - - -
385A ARG* 3.3 25.0 - - + +
387A GLY 4.7 2.8 + - - -
502A VDM 5.0 1.0 + - - -
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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