Contacts of the helix formed by residues 102 - 111 (chain A) in PDB entry 2IB8
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 ALA 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLN* 1.3 80.3 - - + +
103A PRO* 1.3 75.6 - - - +
104A THR 3.3 2.7 - - - -
105A ARG* 3.0 29.6 + - + +
106A GLN 3.1 8.1 + - - -
121A THR* 4.5 1.8 - - - -
123B ASN* 5.4 5.4 - - - +
125B VAL* 3.7 26.1 - - + +
182B ASP 4.7 0.6 + - - -
188B TYR* 5.6 0.4 - - - +
414B ASN* 5.9 0.4 - - - +
415B GLY 4.2 10.3 - - - +
416B GLY* 5.1 1.6 - - - -
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Residues in contact with PRO 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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65A THR* 3.4 19.4 - - + +
93A ASN* 3.5 13.0 - - - +
96A GLN* 4.6 11.4 - - + +
99A GLU* 3.3 31.6 - - + +
100A GLY 3.9 12.8 - - - +
102A ALA* 1.3 86.2 - - - +
104A THR* 1.3 62.1 + - - +
106A GLN* 3.2 5.7 + - - +
107A ALA 3.0 17.8 + - - -
121A THR* 3.8 13.5 - - - +
153A MET* 3.6 11.5 - - + +
123B ASN* 4.3 15.0 - - - +
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Residues in contact with THR 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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89A ALA* 3.8 16.2 - - + +
91A MET* 3.4 35.1 + - + +
102A ALA 3.3 0.4 - - - -
103A PRO* 1.3 74.0 - - - +
105A ARG* 1.3 63.9 + - - +
107A ALA* 3.2 4.0 + - - +
108A VAL* 3.0 23.9 + - + +
119A CYS* 3.8 15.5 - - + -
120A THR* 3.2 24.8 + - - +
121A THR* 2.7 30.8 + - - +
153A MET* 4.1 5.8 - - - +
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Residues in contact with ARG 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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102A ALA* 3.0 23.1 + - + +
104A THR* 1.3 79.3 - - - +
106A GLN* 1.3 56.2 + - - +
108A VAL* 3.3 0.9 + - - +
109A LEU* 2.8 60.5 + - + +
114A PRO 4.2 0.8 + - - -
115A ILE* 2.9 29.9 + - - +
117A THR* 2.9 29.3 + - - +
119A CYS* 3.6 24.6 - - + +
2002A CL 4.2 10.2 - - - +
188B TYR* 3.3 12.6 - - - +
319B ALA* 3.7 10.6 - - - +
320B VAL 2.9 27.5 + - - +
322B PRO* 4.3 1.8 - - - +
415B GLY 5.4 0.2 - - - +
416B GLY* 2.8 36.4 + - - +
417B GLY* 4.3 0.4 - - - -
418B GLY 5.4 0.2 - - - -
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Residues in contact with GLN 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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65A THR* 3.7 23.2 + - + +
69A SER* 3.8 1.2 + - - -
99A GLU 2.9 28.7 + - - +
100A GLY 3.5 8.5 + - - -
101A GLN 3.0 27.0 + - - +
102A ALA 3.1 5.8 + - - +
103A PRO* 3.2 14.0 + - - +
105A ARG* 1.3 77.2 - - - +
107A ALA* 1.3 56.7 + - - +
109A LEU* 4.4 0.2 - - - +
110A GLY* 2.9 26.7 + - - -
187B VAL* 3.7 26.6 - - + +
188B TYR* 3.2 21.7 + - + +
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Residues in contact with ALA 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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65A THR* 3.6 16.3 - - - +
68A GLY 4.1 0.4 - - - -
69A SER* 2.6 34.9 + - - +
72A ILE* 3.9 19.0 - - + +
91A MET* 5.1 2.0 - - + -
103A PRO 3.0 12.6 + - - +
104A THR* 3.2 10.1 + - - +
106A GLN* 1.3 75.0 - - - +
108A VAL* 1.3 58.4 + - - +
111A ALA* 3.1 13.5 + - - +
153A MET* 4.1 17.5 - - - -
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Residues in contact with VAL 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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72A ILE* 4.0 17.7 - - + -
89A ALA* 3.4 31.2 - - + -
104A THR* 3.0 20.6 + - + +
105A ARG 3.7 0.9 - - - +
107A ALA* 1.3 73.3 - - - +
109A LEU* 1.3 72.3 + - + +
111A ALA* 3.2 10.5 + - - +
113A LEU* 3.2 47.4 + - + +
117A THR* 3.9 18.4 - - + +
119A CYS* 3.7 19.7 - - - -
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Residues in contact with LEU 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 ARG* 2.8 56.7 + - - +
108A VAL* 1.3 74.8 - - + +
110A GLY* 1.3 57.6 + - - +
112A GLY* 3.0 19.4 + - - -
113A LEU 3.7 20.1 - - - +
114A PRO 4.0 6.5 - - - +
115A ILE* 4.1 15.7 - - + +
188B TYR* 3.6 41.5 - - + +
322B PRO* 4.0 15.3 - - + -
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Residues in contact with GLY 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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66A LYS* 5.3 5.4 + - - -
69A SER* 3.4 22.3 + - - -
73A GLN* 5.1 1.7 - - - +
106A GLN 2.9 15.2 + - - -
108A VAL 3.2 0.2 - - - -
109A LEU* 1.3 78.3 - - - +
111A ALA* 1.3 55.5 + - - +
112A GLY 3.2 1.6 + - - -
188B TYR* 5.7 0.4 - - - -
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Residues in contact with ALA 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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69A SER* 3.6 23.6 - - - +
72A ILE* 4.0 11.2 - - + -
73A GLN* 4.0 15.0 - - + +
83A LYS* 2.7 35.6 + - - +
107A ALA 3.1 15.9 + - - +
108A VAL 3.2 6.7 + - - +
110A GLY* 1.3 75.3 - - - +
112A GLY* 1.3 53.7 + - - +
113A LEU* 3.4 14.0 + - + -
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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