Contacts of the helix formed by residues 82 - 93 (chain A) in PDB entry 1C7Y
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 GLY 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ILE* 4.0 9.6 - - - -
80A GLY 4.1 1.2 + - - -
81A VAL* 1.3 74.9 - - - +
83A PRO* 1.3 77.7 - - - +
84A LYS 3.3 3.0 + - - -
85A LEU* 3.3 8.3 + - - +
86A ALA* 3.1 22.9 + - - +
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Residues in contact with PRO 83 (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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50A HIS* 5.7 0.4 - - + -
52A VAL* 4.3 17.3 - - + -
61A TYR* 3.3 41.9 - - + +
72A PHE* 3.6 19.5 - - + -
76A ILE* 4.0 10.7 - - + -
82A GLY* 1.3 81.6 - - - +
84A LYS* 1.3 58.8 + - - +
86A ALA 3.5 0.2 + - - -
87A LEU* 2.9 30.8 + - - +
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Residues in contact with LYS 84 (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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61A TYR* 4.4 4.8 + - - +
82A GLY 3.3 0.8 - - - -
83A PRO* 1.3 80.7 - - - +
85A LEU* 1.3 60.2 + - + +
87A LEU* 3.1 10.8 + - + +
88A ALA* 2.8 29.2 + - + +
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Residues in contact with LEU 85 (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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80A GLY 3.0 29.6 - - - +
81A VAL* 3.6 21.1 - - + -
82A GLY 3.3 12.2 + - - +
84A LYS* 1.3 79.8 - - + +
86A ALA* 1.3 54.1 + - - +
88A ALA* 2.9 8.2 + - + +
89A ILE* 2.6 42.9 + - + +
114A PRO 4.2 10.3 - - - +
115A GLY* 3.9 30.5 - - - +
116A ILE* 4.1 13.5 - - + -
120A THR* 5.5 4.3 - - + -
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Residues in contact with ALA 86 (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 PHE* 3.5 29.8 - - + -
75A LEU* 4.0 24.5 - - + -
76A ILE* 4.2 4.7 - - + -
81A VAL* 4.2 2.2 - - + +
82A GLY 3.1 12.0 + - - +
85A LEU* 1.3 78.3 - - - +
87A LEU* 1.3 58.2 + - - +
89A ILE* 3.3 14.3 - - - +
90A LEU* 2.8 34.0 + - - +
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Residues in contact with LEU 87 (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 PRO* 4.2 26.5 - - + -
29A HIS* 3.9 24.0 - - + +
30A MET 4.5 2.5 - - - +
31A PRO* 4.1 16.1 - - + +
61A TYR* 3.6 35.0 - - + -
72A PHE* 4.1 5.8 - - + -
83A PRO 2.9 12.5 + - - +
84A LYS* 3.3 13.5 - - + +
85A LEU 3.1 0.2 - - - -
86A ALA* 1.3 73.9 - - - +
88A ALA* 1.3 61.7 + - - +
90A LEU* 3.1 10.7 + - - +
91A SER* 2.7 33.3 + - - +
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Residues in contact with ALA 88 (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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84A LYS* 2.8 15.8 + - + +
85A LEU* 3.3 10.3 - - + +
87A LEU* 1.3 79.3 - - + +
89A ILE* 1.3 55.5 + - + +
91A SER* 2.7 30.4 + - - -
92A GLY* 3.0 10.9 + - - -
113A LEU* 4.9 5.4 - - + +
114A PRO* 4.3 30.4 - - + +
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Residues in contact with ILE 89 (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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75A LEU* 4.6 18.6 - - + -
81A VAL* 4.9 8.3 - - + -
85A LEU* 2.6 32.1 + - + +
86A ALA* 3.3 17.3 - - - +
88A ALA* 1.3 74.3 - - + +
90A LEU* 1.3 66.3 + - + +
92A GLY* 3.6 0.9 + - - -
93A MET* 3.1 30.2 + - + +
98A PHE* 4.1 28.7 - - + -
110A LEU* 5.3 0.7 - - + -
113A LEU* 4.3 22.5 - - + +
116A ILE* 4.3 26.5 - - + -
124A LEU* 4.9 12.8 - - + -
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Residues in contact with LEU 90 (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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31A PRO* 3.1 33.7 - - + +
33A THR* 3.1 20.9 + - - +
34A CYS* 5.8 2.0 - - - -
63A PHE* 4.8 1.8 - - + -
68A GLU* 4.5 7.0 - - + +
71A LEU* 3.8 20.9 - - + -
72A PHE* 4.2 20.9 - - + -
75A LEU* 3.9 24.2 - - + -
86A ALA 2.8 18.8 + - - +
87A LEU 3.1 4.4 + - - -
89A ILE* 1.3 78.8 - - + +
91A SER* 1.3 57.4 + - - +
93A MET 3.3 16.6 - - - +
94A SER* 4.1 1.6 - - - +
95A ALA* 3.7 21.8 - - + +
98A PHE* 4.9 3.8 - - + -
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Residues in contact with SER 91 (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 PRO* 5.7 0.2 - - - +
31A PRO* 3.9 1.4 - - - +
32A MET* 3.2 47.3 + - - +
33A THR* 4.0 7.5 - - - +
36A TYR* 4.4 6.6 + - - -
87A LEU* 2.7 26.6 + - - +
88A ALA* 2.7 11.9 + - - -
90A LEU* 1.3 76.7 - - - +
92A GLY* 1.3 66.2 + - - +
93A MET 3.4 0.2 - - - -
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Residues in contact with GLY 92 (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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33A THR* 5.0 1.1 - - - +
88A ALA 3.0 11.3 + - - -
89A ILE 4.2 1.1 - - - -
91A SER* 1.3 81.6 - - - +
93A MET* 1.3 60.2 + - - +
97A GLN* 4.2 4.0 - - - +
113A LEU* 4.4 16.4 - - - -
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Residues in contact with MET 93 (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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33A THR* 3.7 6.3 - - - -
89A ILE* 3.1 26.4 + - + +
90A LEU* 3.3 16.3 - - - +
92A GLY* 1.3 80.4 - - - +
94A SER* 1.3 61.2 + - - +
97A GLN* 3.5 26.9 - - + +
98A PHE* 3.5 44.6 - - + +
101A ALA* 4.3 5.2 - - + -
106A GLU* 5.7 0.7 - - - +
109A ALA* 3.8 29.2 - - + +
110A LEU* 3.7 21.1 - - + -
113A LEU* 4.9 7.0 - - + -
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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