Contacts of the helix formed by residues 101 - 108 (chain C) in PDB entry 5GV2
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 VAL 101 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C LEU* 4.9 3.6 - - + -
79C LEU* 5.6 1.6 - - + -
81C VAL* 4.2 13.5 - - + -
97C ILE* 2.9 31.0 + - + +
99C ARG 3.6 0.2 - - - -
100C SER* 1.3 88.7 - - - +
102C ILE* 1.3 66.1 + - + +
103C ALA 3.6 1.3 - - - -
104C PRO* 3.5 3.1 - - - +
105C LEU* 3.1 48.5 + - + +
123C ILE* 4.7 15.5 - - + -
137C LEU* 4.1 15.7 - - + +
141C PHE* 3.6 26.0 - - + -
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Residues in contact with ILE 102 (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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94C VAL* 3.6 44.0 - - + +
97C ILE* 3.0 19.8 + - + +
98C ALA* 3.7 13.5 - - + +
101C VAL* 1.3 76.2 - - + +
103C ALA* 1.3 65.1 + - - +
105C LEU* 3.3 6.2 + - - +
106C ALA* 3.0 22.6 + - + +
112C VAL* 5.5 8.5 - - + +
114C MET* 4.5 11.9 - - + -
123C ILE* 5.4 2.7 - - + -
281C VAL* 3.9 20.0 - - + +
282C ALA* 3.6 32.5 - - + +
285C ALA* 4.2 4.0 - - + -
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Residues in contact with ALA 103 (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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98C ALA 2.8 21.7 + - - +
99C ARG* 4.4 4.9 - - - +
102C ILE* 1.3 73.0 - - - +
104C PRO* 1.4 63.7 - - + +
106C ALA* 3.3 2.1 + - - +
107C GLU* 2.8 31.6 + - - +
282C ALA* 4.4 15.0 - - + +
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Residues in contact with PRO 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 ARG 3.2 25.8 - - - +
100C SER* 3.6 14.4 - - - +
101C VAL 3.5 12.3 - - - +
103C ALA* 1.4 91.7 - - + +
105C LEU* 1.3 59.9 + - - +
107C GLU* 3.3 7.0 + - + -
108C HIS* 2.6 35.3 + - + +
136C THR* 3.5 23.3 - - + +
137C LEU* 4.6 1.8 - - + -
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Residues in contact with LEU 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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79C LEU* 4.7 3.8 - - + -
101C VAL* 3.1 39.9 + - + +
102C ILE* 3.3 4.5 + - - +
104C PRO* 1.3 76.9 - - - +
106C ALA* 1.3 61.4 + - - +
108C HIS* 3.2 6.6 + - - -
110C VAL* 2.9 46.7 + - + +
112C VAL* 3.9 23.6 - - + -
123C ILE* 4.6 5.2 - - + -
125C VAL* 4.4 12.3 - - + -
133C VAL* 3.9 33.9 - - + -
136C THR* 4.4 8.7 - - - -
137C LEU* 4.2 18.8 - - + -
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Residues in contact with ALA 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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102C ILE* 3.0 17.3 + - + +
103C ALA* 3.7 3.8 - - - +
105C LEU* 1.3 75.1 - - - +
107C GLU* 1.3 62.1 + - - +
109C HIS* 3.0 19.9 + - - -
110C VAL 4.2 2.2 + - - -
112C VAL* 5.9 0.2 - - - +
278C CYS* 4.2 13.5 - - - +
279C GLY* 3.6 32.3 - - - +
282C ALA* 4.1 10.5 - - + -
401C ARG 5.9 0.4 - - - +
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Residues in contact with GLU 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 ALA 2.8 22.0 + - - +
104C PRO* 3.6 10.1 - - + +
105C LEU 3.3 0.2 - - - -
106C ALA* 1.3 73.2 - - - +
108C HIS* 1.3 68.9 + - + +
109C HIS* 3.4 13.8 + - - -
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Residues in contact with HIS 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 PRO* 2.6 29.4 + - + +
105C LEU 3.2 3.8 + - - +
106C ALA 3.1 0.6 - - - -
107C GLU* 1.3 87.3 - - + +
109C HIS* 1.3 76.6 + - - +
110C VAL* 3.3 7.6 + - + +
132C VAL* 3.9 18.5 - - + +
135C HIS* 3.4 12.2 + + - -
136C THR* 3.4 34.3 - - + +
501C MG 2.3 31.9 - - - -
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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