Contacts of the helix formed by residues 105 - 116 (chain A) in PDB entry 2G2B
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 SER 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TYR* 3.9 4.5 - - - -
65A ASN* 5.4 6.5 + - - -
66A GLY 5.6 0.4 - - - -
67A ASP* 5.5 3.1 - - - +
103A THR 5.4 0.2 + - - -
104A PHE* 1.3 86.1 + - - +
106A TYR* 1.3 66.7 + - - +
107A PRO* 3.4 9.9 - - - -
108A ASP* 3.2 27.3 + - - +
109A PHE 3.1 18.0 + - - -
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Residues in contact with TYR 106 (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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27A LEU* 3.3 26.7 - - + -
30A ILE* 3.4 39.7 - - + -
31A ASN* 2.7 31.6 + - - -
50A LEU 3.5 1.4 + - - -
53A PHE* 3.5 30.6 - + - -
54A LYS* 3.1 27.8 - - - +
57A TYR* 3.2 59.2 + + + +
105A SER* 1.3 71.6 - - - +
107A PRO* 1.4 68.1 - - + +
109A PHE* 3.3 5.9 + - - +
110A LEU* 3.3 20.2 + - + +
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Residues in contact with PRO 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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30A ILE* 4.0 22.9 - - + -
33A GLN* 5.4 2.7 - - - +
34A PHE* 4.0 26.5 - - + -
105A SER* 3.5 12.6 - - - -
106A TYR* 1.4 94.8 - - + +
108A ASP* 1.3 52.8 + - - +
110A LEU* 3.1 5.6 + - + +
111A ARG* 2.8 48.5 + - - +
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Residues in contact with ASP 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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96A VAL* 3.5 33.9 - - + +
97A SER* 5.3 3.6 - - - -
105A SER* 3.2 32.3 + - - +
107A PRO* 1.3 76.4 - - - +
109A PHE* 1.3 65.6 + - - +
111A ARG* 3.2 17.3 + - + +
112A MET* 3.1 23.7 + - - +
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Residues in contact with PHE 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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53A PHE* 3.4 41.5 - + + -
73A LEU* 6.1 2.0 - - + -
96A VAL* 3.6 9.3 - - + +
104A PHE* 3.5 29.8 - + + -
105A SER 3.1 10.8 + - - +
106A TYR 3.5 2.5 - - - +
107A PRO 3.3 0.2 - - - -
108A ASP* 1.3 76.4 - - - +
110A LEU* 1.3 58.5 + - - +
112A MET* 3.4 6.5 + - + +
113A MET* 3.0 58.7 + - + +
121A LEU* 3.4 42.2 - - + -
124A ILE* 6.1 0.7 - - + -
125A LEU* 3.8 23.1 - - + -
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Residues in contact with LEU 110 (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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30A ILE* 4.1 3.1 - - + +
31A ASN* 4.1 8.1 - - - +
34A PHE* 4.0 28.0 - - + -
50A LEU* 4.0 18.8 - - + -
53A PHE* 3.5 24.0 - - + -
106A TYR* 3.3 35.8 + - + +
107A PRO* 3.1 9.1 + - + +
109A PHE* 1.3 76.4 - - - +
111A ARG* 1.3 56.2 + - - +
113A MET* 3.9 11.4 - - + -
114A LEU* 2.7 65.0 + - + +
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Residues in contact with ARG 111 (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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34A PHE* 3.7 35.2 - - - -
39A LYS* 5.4 6.3 - - - +
40A TYR* 5.4 7.7 + - - -
107A PRO* 2.8 36.8 + - - +
108A ASP* 3.3 22.8 + - - +
110A LEU* 1.3 72.2 - - - +
112A MET* 1.3 58.9 + - - +
114A LEU* 5.0 1.8 - - - -
115A GLY* 2.9 26.9 + - - -
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Residues in contact with MET 112 (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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95A GLU* 5.2 1.1 - - + -
96A VAL* 4.4 13.0 - - + -
108A ASP 3.1 12.9 + - - +
109A PHE* 3.6 7.4 - - + +
111A ARG* 1.3 80.1 - - - +
113A MET* 1.3 86.5 + - + +
115A GLY* 4.1 0.2 - - - -
116A LYS 3.4 5.2 + - - -
117A ARG* 3.4 19.5 + - - -
118A SER* 3.4 23.5 + - - -
119A ALA* 3.3 37.5 - - + +
121A LEU* 3.5 31.6 - - + -
122A LYS* 3.8 11.9 - - + -
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Residues in contact with MET 113 (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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49A LYS* 4.8 18.4 - - + +
53A PHE* 4.2 13.9 - - + -
109A PHE* 3.0 43.3 + - + +
110A LEU* 3.9 21.5 - - + -
112A MET* 1.3 95.3 - - + +
114A LEU* 1.3 70.8 + - + +
115A GLY 3.5 0.2 + - - -
116A LYS* 3.6 5.4 + - - +
122A LYS* 2.9 55.4 + - + +
125A LEU* 3.9 18.4 - - + -
126A MET* 5.5 0.9 - - - -
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Residues in contact with LEU 114 (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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34A PHE* 3.8 37.5 - - + -
40A TYR* 3.5 36.8 - - + +
46A LEU* 3.8 25.6 - - + -
49A LYS* 6.1 2.7 - - + -
50A LEU* 4.3 11.0 - - + -
110A LEU* 2.7 49.1 + - + +
111A ARG 4.6 0.2 - - - +
113A MET* 1.3 81.1 - - + +
115A GLY* 1.3 66.0 + - - +
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Residues in contact with GLY 115 (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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40A TYR* 5.2 2.2 + - - -
111A ARG 2.9 21.6 + - - -
112A MET* 4.1 0.4 - - - -
113A MET 3.2 0.2 - - - -
114A LEU* 1.3 83.0 - - - +
116A LYS* 1.3 67.7 + - - +
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Residues in contact with LYS 116 (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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112A MET 3.4 6.5 + - - -
113A MET 3.6 2.6 - - - +
114A LEU 3.6 0.4 - - - -
115A GLY* 1.3 81.3 - - - +
117A ARG* 1.3 90.2 + - + +
118A SER* 5.3 3.1 - - - +
122A LYS* 2.7 29.4 + - - +
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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