Contacts of the helix formed by residues 100 - 111 (chain A) in PDB entry 1Y02
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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98A CYS* 4.6 1.3 - - - +
99A ARG* 1.3 88.2 + - + +
101A LYS* 1.3 66.3 + - - +
102A GLU* 3.2 15.7 - - + +
103A GLU* 2.9 35.5 + - + +
104A LEU* 3.7 5.7 + - - +
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Residues in contact with LYS 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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77A MET* 2.7 40.5 + - - +
78A LYS* 4.2 2.2 + - - +
79A MET 2.7 30.0 + - - +
80A LYS* 4.9 0.6 - - - +
81A VAL* 4.2 26.1 - - + +
84A LEU* 3.7 20.4 - - + -
100A GLU* 1.3 72.6 - - - +
102A GLU* 1.3 63.6 + - - +
104A LEU* 2.9 23.6 + - + +
105A VAL* 3.2 10.0 + - - +
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Residues in contact with GLU 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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73A ARG* 3.6 26.3 + - - +
77A MET* 4.1 22.9 - - + +
100A GLU* 3.2 14.9 - - + +
101A LYS* 1.3 77.6 - - - +
103A GLU* 1.3 58.8 + - + +
105A VAL* 3.2 3.7 + - + +
106A LEU* 2.9 45.4 + - + +
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Residues in contact with GLU 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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97A MET 3.6 7.6 - - - +
98A CYS* 3.4 27.1 - - - -
99A ARG* 2.8 29.8 + - - +
100A GLU* 2.9 27.7 + - + +
102A GLU* 1.3 79.2 - - + +
104A LEU* 1.3 62.6 + - - +
106A LEU* 3.3 15.0 + - + +
107A LEU* 3.1 26.5 + - - +
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Residues in contact with LEU 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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81A VAL* 3.9 29.2 - - + +
84A LEU* 4.1 29.2 - - + -
85A ARG* 4.7 9.2 - - + +
88A LEU* 3.6 8.2 - - + +
95A THR* 3.6 38.4 - - + +
98A CYS* 3.9 13.5 - - + -
100A GLU 4.4 6.3 - - - +
101A LYS* 2.9 20.0 + - + +
103A GLU* 1.3 76.4 - - - +
105A VAL* 1.3 65.2 + - - +
107A LEU* 3.1 5.5 + - - +
108A VAL* 3.0 27.0 + - - +
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Residues in contact with VAL 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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73A ARG* 4.3 15.5 - - - +
76A LEU* 4.0 37.2 - - + +
77A MET* 3.8 31.0 - - + -
84A LEU* 4.2 11.4 - - + -
101A LYS 3.2 11.1 + - - +
102A GLU* 3.2 8.5 + - + +
104A LEU* 1.3 77.7 - - - +
106A LEU* 1.3 58.0 + - + +
108A VAL* 3.2 9.6 + - - +
109A LEU* 2.9 43.6 + - + +
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Residues in contact with LEU 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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73A ARG* 5.7 4.3 - - - +
102A GLU* 2.9 34.1 + - + +
103A GLU* 3.6 17.5 - - + +
104A LEU 3.2 0.2 - - - -
105A VAL* 1.3 76.5 - - + +
107A LEU* 1.3 59.4 + - + +
109A LEU* 3.3 19.6 + - + +
110A GLY* 2.9 25.3 + - - -
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Residues in contact with LEU 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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88A LEU* 3.8 25.7 - - + +
93A ILE* 4.3 15.2 - - + +
94A SER 3.9 16.8 - - - +
95A THR* 4.2 0.7 - - + -
98A CYS* 3.6 31.2 - - - -
103A GLU 3.1 13.2 + - - +
104A LEU* 3.1 7.1 + - - +
106A LEU* 1.3 75.0 - - + +
108A VAL* 1.3 66.2 + - - +
110A GLY* 3.3 1.9 + - - +
111A GLN* 3.2 24.9 + - - +
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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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66A PHE* 3.9 27.6 - - + -
71A PHE* 3.9 16.7 - - + -
76A LEU* 4.0 16.6 - - + -
84A LEU* 3.9 22.4 - - + +
87A TYR* 4.0 7.9 - - + -
88A LEU* 3.9 24.7 - - + -
104A LEU 3.0 18.1 + - - +
105A VAL 3.5 7.2 - - - +
107A LEU* 1.3 77.5 - - - +
109A LEU* 1.3 62.1 + - - +
110A GLY 3.3 0.2 + - - -
111A GLN* 3.0 24.5 + - - -
112A GLN* 3.4 5.2 + - - +
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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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71A PHE* 3.2 31.9 - - + +
73A ARG* 4.4 19.5 - - + +
76A LEU* 3.5 16.6 - - + -
105A VAL* 2.9 31.1 + - + +
106A LEU* 3.6 22.4 - - + +
108A VAL* 1.3 77.9 - - - +
110A GLY* 1.3 62.3 + - - +
112A GLN* 3.2 28.5 + - - +
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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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106A LEU 2.9 16.5 + - - -
107A LEU* 3.3 3.6 + - - -
108A VAL 3.2 0.4 - - - -
109A LEU* 1.3 77.7 - - - +
111A GLN* 1.3 58.4 + - - +
112A GLN 3.2 4.0 + - - +
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Residues in contact with GLN 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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71A PHE* 3.7 9.3 - - - -
87A TYR* 3.4 29.7 + - - -
88A LEU* 4.5 3.4 - - + -
91A HIS* 3.4 29.3 + - + -
93A ILE* 3.6 29.6 - - + -
107A LEU 3.2 12.0 + - - +
108A VAL* 3.0 24.4 + - - +
110A GLY* 1.3 72.6 - - - +
112A GLN* 1.3 68.9 + - - +
113A PRO* 3.3 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