Contacts of the helix formed by residues 103 - 109 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98C GLY 3.6 19.3 - - - +
99C PHE* 3.0 32.5 + - + +
101C ASN 3.6 0.2 - - - -
102C SER* 1.3 85.6 - - - +
104C LEU* 1.3 65.7 + - - +
105C TRP 3.5 1.1 - - - -
106C PRO* 3.3 4.5 - - - +
107C LEU* 3.2 23.6 + - - +
113C GLY* 4.9 10.3 - - - +
114C GLU* 6.0 2.9 - - + -
117C PHE* 4.3 15.7 - - + -
118C ASP* 4.1 31.6 - - + +
121C ALA* 4.6 0.2 - - + -
191C LEU* 3.8 26.2 - - + -
192C PRO* 5.8 0.4 - - + -
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Residues in contact with LEU 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C PHE* 3.0 32.0 + - + +
100C SER* 3.4 11.7 - - - +
103C ILE* 1.3 75.9 - - - +
105C TRP* 1.3 66.8 + - - +
107C LEU* 3.3 6.8 + - + +
108C LEU* 3.0 49.2 + - + +
125C TYR* 3.9 12.8 - - + +
151C TYR* 3.2 39.7 - - + +
154C MET* 4.2 10.3 - - - -
188C TYR* 5.5 2.0 - - + -
191C LEU* 4.4 9.9 - - + -
197C LEU* 4.0 18.6 - - + -
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Residues in contact with TRP 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C SER 2.8 20.4 + - - +
101C ASN* 3.9 9.4 - - - -
104C LEU* 1.3 74.2 - - - +
106C PRO* 1.3 68.3 - - + +
108C LEU* 3.4 4.8 + - - +
109C HIS* 2.6 54.5 + + - -
151C TYR* 3.4 24.7 - + + -
180C THR* 3.6 15.0 - - + -
287C ARG* 3.4 31.0 - - - -
289C ASP* 3.4 13.1 + - - -
290C TYR* 3.5 18.6 - + - -
291C ILE* 3.5 25.5 - - + +
325C ARG* 3.2 13.5 - - - +
331C TYR* 3.2 19.4 + + - -
502C VDM 3.7 33.7 - - + -
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Residues in contact with PRO 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ASN 3.5 13.9 - - - +
102C SER* 3.2 24.0 - - - +
103C ILE* 3.3 14.4 - - - +
105C TRP* 1.3 97.5 - - + +
107C LEU* 1.3 59.5 + - - +
109C HIS* 3.1 5.9 + - + -
111C HIS* 2.8 49.9 + - + +
112C PRO 4.5 1.8 - - - +
113C GLY* 4.5 13.7 - - - -
290C TYR* 3.5 21.5 - - + +
330C GLU* 6.1 1.3 - - + -
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Residues in contact with LEU 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ILE* 3.2 18.5 + - + +
104C LEU* 3.8 9.9 - - + +
106C PRO* 1.3 77.9 - - - +
108C LEU* 1.3 64.6 + - + +
110C TYR* 3.1 11.0 + - - +
111C HIS 4.0 6.5 + - - +
183C PRO* 3.9 3.1 - - + +
187C ILE* 3.6 39.7 - - + +
188C TYR* 3.8 27.4 - - + +
190C ILE* 3.8 26.0 - - + -
191C LEU* 3.7 37.9 - - + +
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Residues in contact with LEU 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C LEU* 3.0 37.2 + - + +
105C TRP* 3.8 6.3 - - - +
107C LEU* 1.3 79.9 - - + +
109C HIS* 1.3 62.7 + - - +
110C TYR* 3.4 3.3 + - - -
151C TYR* 3.8 31.0 - - + -
154C MET* 5.6 4.0 - - - -
178C LEU* 4.8 3.1 - - + -
180C THR* 3.4 27.4 - - + +
181C PRO* 3.9 27.4 - - - +
182C PHE* 4.5 14.1 - - + -
183C PRO* 3.8 34.5 - - + +
188C TYR* 5.1 3.1 - - + -
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Residues in contact with HIS 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C TRP* 2.6 70.6 + + - +
106C PRO* 3.1 6.4 + - + +
108C LEU* 1.3 78.2 - - + +
110C TYR* 1.3 76.0 + - - +
111C HIS* 3.1 8.6 + - + +
180C THR* 3.8 16.2 - - - -
181C PRO* 3.3 28.1 - - + +
291C ILE* 3.5 39.0 - - + +
384C THR* 5.5 0.7 + - - -
385C ARG* 3.4 23.2 - - + +
386C ASP 4.7 0.2 - - - -
387C GLY 4.8 2.2 + - - -
502C VDM 5.0 0.6 + - - -
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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