Contacts of the helix formed by residues 97 - 106 (chain A) in PDB entry 2LI6
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 LEU 97 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A CYS 5.0 7.0 - - - +
35A ASN* 3.2 38.8 - - + +
93A PHE* 2.8 35.2 + - + +
94A ARG* 3.2 31.0 - - + +
95A ILE 3.3 1.0 - - - -
96A LEU* 1.3 87.5 - - - +
98A PRO* 1.3 77.5 - - + +
99A TYR* 3.4 14.4 - - + +
100A GLU* 4.3 8.7 - - + +
101A ARG* 3.0 24.1 + - - +
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Residues in contact with PRO 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A LEU 3.6 0.4 - - - +
97A LEU* 1.3 100.6 - - + +
99A TYR* 1.3 81.1 + - + +
101A ARG* 3.5 12.8 - - + -
102A HIS* 2.9 46.9 + - + +
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Residues in contact with TYR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A CYS* 3.1 29.6 - - + +
34A ARG* 5.9 12.3 - - + +
35A ASN* 5.4 5.8 - - - -
97A LEU* 4.8 14.6 - - + -
98A PRO* 1.3 97.8 - - + +
100A GLU* 1.3 59.8 + - - +
102A HIS* 3.6 6.8 - + - +
103A MET* 3.0 25.3 + - - +
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Residues in contact with GLU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 2.9 47.4 - - + +
31A CYS* 3.2 28.5 - - + -
32A LYS* 3.0 27.1 - - - +
94A ARG 2.6 34.9 - - - +
95A ILE* 3.4 20.5 + - - +
97A LEU* 3.7 5.8 + - + +
98A PRO 3.4 0.2 - - - -
99A TYR* 1.3 80.2 - - - +
101A ARG* 1.3 61.1 + - - +
103A MET* 3.4 3.9 + - - +
104A ILE* 3.3 29.8 + - - +
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Residues in contact with ARG 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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95A ILE 4.3 4.4 + - - +
96A LEU* 3.8 13.1 + - + +
97A LEU 3.0 25.5 + - - +
98A PRO* 3.1 18.4 - - - +
100A GLU* 1.3 76.6 - - - +
102A HIS* 1.3 78.2 + - - +
104A ILE* 2.9 18.5 - - + +
105A SER* 2.7 37.0 + - - -
111A GLU 5.6 0.6 + - - -
112A THR* 4.5 33.5 + - - +
116A ARG* 3.3 30.1 - - - +
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Residues in contact with HIS 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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98A PRO* 2.9 33.4 + - + +
99A TYR* 3.6 8.3 - + - +
100A GLU 3.2 0.2 - - - -
101A ARG* 1.3 100.5 + - + +
103A MET* 1.3 65.4 + - + +
105A SER* 3.0 22.6 + - - -
106A GLN* 3.4 11.4 + - - +
112A THR* 6.5 0.2 - - + -
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Residues in contact with MET 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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27A LEU* 3.1 57.0 - - + +
30A ASN* 6.2 4.3 - - + +
31A CYS* 3.5 26.7 - - - -
99A TYR 3.0 11.8 + - - +
100A GLU 3.7 5.4 - - - +
102A HIS* 1.3 76.4 - - - +
104A ILE* 1.3 61.0 + - + +
106A GLN* 3.8 23.4 - - - +
107A GLU* 4.7 1.2 + - - +
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Residues in contact with ILE 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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24A MET* 3.6 32.2 - - + +
27A LEU* 4.6 5.2 - - + -
28A ILE* 3.5 29.6 - - + -
51A LEU* 5.2 14.5 - - + +
95A ILE* 5.2 6.5 - - + +
100A GLU 3.3 11.0 - - - +
101A ARG* 2.9 36.6 - - + +
103A MET* 1.3 77.2 - - + +
105A SER* 1.3 65.7 + - - +
106A GLN 3.1 2.2 - - - -
107A GLU* 3.1 17.5 + - - +
108A GLY* 3.5 6.1 + - - -
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Residues in contact with SER 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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101A ARG* 2.7 22.9 + - - -
102A HIS* 3.0 16.4 + - - -
104A ILE* 1.3 76.6 - - - +
106A GLN* 1.3 60.6 + - - +
108A GLY 2.8 10.4 + - - -
109A ILE* 2.7 43.7 + - - +
112A THR* 3.8 18.8 + - - -
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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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102A HIS 3.4 9.0 + - - +
103A MET* 3.8 18.6 - - - +
104A ILE 3.1 0.2 - - - -
105A SER* 1.3 81.9 + - - +
107A GLU* 1.3 59.4 + - - +
108A GLY 3.4 0.2 + - - -
109A ILE* 4.2 13.1 + - + +
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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