Contacts of the helix formed by residues 100 - 110 (chain A) in PDB entry 2IAI
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 GLU 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A ARG* 2.8 47.2 + - - +
64A ALA* 5.3 1.8 - - - -
67A GLU* 4.0 30.2 - - + +
96A VAL* 2.8 21.2 + - + +
97A LEU 3.9 2.2 - - - -
99A ALA* 1.3 90.0 - - + +
101A LEU* 1.3 63.1 + - - +
102A PRO* 3.3 5.6 - - - -
103A TYR* 3.0 19.9 + - + -
104A VAL* 2.9 29.7 + - + -
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Residues in contact with LEU 101 (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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97A LEU* 3.1 23.6 + - + +
98A MSE 3.6 9.6 - - - +
99A ALA 3.5 1.6 - - - -
100A GLU* 1.3 75.6 - - - +
102A PRO* 1.3 68.0 - - + +
104A VAL* 3.9 1.8 - - - +
105A THR* 2.7 36.5 + - - +
165A VAL* 3.7 40.2 - - + +
168A TYR* 4.1 31.2 - - + +
170A PRO* 4.9 8.3 - - + -
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Residues in contact with PRO 102 (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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19A VAL* 3.6 15.3 - - + -
23A ILE* 3.6 25.5 - - + +
99A ALA 5.1 2.2 - - - +
100A GLU 3.4 4.3 - - - -
101A LEU* 1.3 101.6 - - + +
103A TYR* 1.3 70.8 + - + +
105A THR* 3.4 4.4 + - - +
106A LEU* 3.1 32.1 + - - +
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Residues in contact with TYR 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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15A LEU* 4.2 19.5 - - + +
16A SER* 4.4 16.6 - - - -
19A VAL* 3.7 22.7 - - + -
60A ALA* 3.6 38.4 - - + +
61A VAL* 5.0 1.2 - - - +
63A ARG* 3.7 29.5 - - - -
64A ALA* 3.6 16.4 - - + +
100A GLU* 3.0 28.2 + - + +
102A PRO* 1.3 88.4 - - + +
104A VAL* 1.3 66.1 + - - +
106A LEU* 3.3 8.3 + - - +
107A LEU* 3.0 22.0 + - - +
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Residues in contact with VAL 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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64A ALA* 4.0 16.6 - - + -
68A LEU* 4.9 16.4 - - + -
96A VAL* 4.4 10.8 - - + +
97A LEU* 4.3 31.6 - - + +
100A GLU* 2.9 32.5 + - + +
101A LEU* 4.0 2.9 - - - +
103A TYR* 1.3 77.9 - - - +
105A THR* 1.3 62.2 + - - +
107A LEU* 3.2 3.5 + - + +
108A LEU* 2.9 45.3 + - + +
162A ASN* 5.4 1.6 - - - +
165A VAL* 4.4 1.1 - - + -
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Residues in contact with THR 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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23A ILE* 4.6 10.8 - - + -
101A LEU* 2.7 31.3 + - - +
102A PRO* 3.5 8.0 - - - +
104A VAL* 1.3 75.2 - - - +
106A LEU* 1.3 62.9 + - - +
108A LEU* 3.2 6.5 + - - +
109A ARG* 3.1 58.9 + - + +
165A VAL* 3.6 32.8 + - + +
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Residues in contact with LEU 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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19A VAL* 3.9 36.1 - - + -
22A PHE* 3.7 39.0 - - + +
23A ILE* 3.7 24.9 - - + +
27A TYR* 5.7 3.8 - - + +
57A LEU* 4.7 9.0 - - + +
60A ALA* 4.1 10.1 - - + -
61A VAL* 4.4 8.7 - - + -
102A PRO 3.1 15.9 + - - +
103A TYR* 3.3 6.7 + - - +
105A THR* 1.3 72.1 - - - +
107A LEU* 1.3 66.3 + - - +
109A ARG* 3.1 22.0 + - + +
110A VAL* 3.2 17.7 + - - +
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Residues in contact with LEU 107 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A VAL* 4.0 13.4 - - + +
64A ALA* 4.1 13.0 - - + -
65A LEU* 3.7 41.3 - - + -
68A LEU* 3.9 23.1 - - + -
103A TYR 3.0 13.4 + - - +
104A VAL* 3.2 10.5 + - + +
106A LEU* 1.3 75.1 - - - +
108A LEU* 1.3 68.9 + - + +
109A ARG 3.2 0.7 + - - -
110A VAL* 3.3 16.7 + - + +
120A ALA* 4.1 17.7 - - + -
121A LEU* 5.7 0.2 - - - +
124A ARG* 3.8 36.6 + - + +
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Residues in contact with LEU 108 (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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104A VAL* 2.9 37.6 + - + +
105A THR* 3.7 5.4 - - - +
106A LEU 3.2 0.2 - - - -
107A LEU* 1.3 81.0 - - + +
109A ARG* 1.3 58.7 + - + +
110A VAL 3.4 1.6 + - - +
111A ARG* 4.0 12.1 + - - -
124A ARG* 3.3 46.4 + - - +
162A ASN* 3.8 39.7 - - + +
165A VAL* 4.1 22.7 - - + -
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Residues in contact with ARG 109 (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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22A PHE 4.7 1.4 + - - -
23A ILE* 3.1 45.4 + - - +
26A GLY* 5.6 3.8 - - - +
105A THR* 3.1 39.1 + - + +
106A LEU* 3.1 14.5 + - + +
108A LEU* 1.3 76.1 - - + +
110A VAL* 1.3 66.9 + - - +
111A ARG* 3.1 20.2 + - - +
166A GLU* 5.7 6.7 - - - -
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Residues in contact with VAL 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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57A LEU* 5.0 7.6 - - + -
61A VAL* 4.2 14.8 - - + -
106A LEU 3.2 15.8 + - - +
107A LEU* 3.3 18.7 + - - +
108A LEU 4.5 1.9 - - - +
109A ARG* 1.3 75.7 - - - +
111A ARG* 1.3 69.0 + - - +
112A GLY 4.2 0.7 - - - +
117A GLU* 3.4 52.9 - - + +
120A ALA* 4.6 9.6 - - + -
121A LEU* 3.6 26.4 - - + +
124A ARG* 5.6 0.7 + - - -
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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