Contacts of the helix formed by residues 102 - 115 (chain A) in PDB entry 3PIT
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 HIS 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ASP* 2.6 38.5 + - - +
72A GLU* 3.5 27.5 + - + -
98A ALA* 3.0 33.2 + - + +
99A SER 4.0 4.0 - - - +
100A PHE 3.1 0.4 - - - -
101A GLU* 1.3 81.7 + - + +
103A VAL* 1.3 64.5 + - - +
104A ASP 3.1 2.9 - - - -
105A ARG* 3.0 30.2 + - + +
106A PHE* 3.3 19.2 + - + -
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Residues in contact with VAL 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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90A ILE* 4.1 24.1 - - + +
91A VAL 5.3 0.9 - - - +
92A TYR* 3.8 16.2 - - + -
99A SER 3.7 12.6 + - - +
100A PHE* 3.1 20.9 + - + +
102A HIS* 1.3 77.4 - - - +
104A ASP* 1.3 58.0 + - - +
106A PHE* 3.2 6.1 + - + +
107A HIS* 2.9 25.8 + - - +
123A LEU* 3.7 33.0 - - + -
144A MET* 4.1 10.1 - - + -
148A TYR* 3.9 23.6 - - + -
150A ILE* 6.0 0.4 - - + -
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Residues in contact with ASP 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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101A GLU 3.5 11.2 + - - +
102A HIS 3.1 1.2 - - - -
103A VAL* 1.3 79.8 - - - +
105A ARG* 1.3 57.9 + - - +
107A HIS* 3.6 2.4 + - - +
108A GLN* 2.8 41.2 + - - +
144A MET* 5.0 4.1 - - + -
147A LYS* 4.1 11.2 + - - +
148A TYR* 2.7 37.9 + - - +
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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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72A GLU* 3.2 31.7 + - - +
73A GLU* 2.8 44.1 + - - +
74A PHE* 4.7 4.6 - - - +
78A ARG* 6.3 0.2 - - - +
101A GLU 4.8 0.2 + - - -
102A HIS* 3.0 27.9 + - + +
104A ASP* 1.3 80.0 + - - +
106A PHE* 1.3 60.5 + - + +
108A GLN* 3.5 10.1 + - - +
109A LEU* 3.0 52.2 + - + +
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Residues in contact with PHE 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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19A VAL* 3.8 22.7 - - + -
20A GLY* 3.5 39.9 - - - -
21A ASP* 3.5 22.7 - - - -
71A GLN 4.0 5.2 - - - -
72A GLU* 5.6 1.1 - - - -
78A ARG* 3.4 36.1 - - - -
82A MET* 4.1 12.1 - - + -
90A ILE* 4.0 18.8 - - + -
91A VAL 5.8 0.2 - - - -
99A SER 5.6 1.8 - - - -
102A HIS* 3.3 27.3 + - + -
103A VAL* 3.2 8.8 + - + +
105A ARG* 1.3 77.5 - - + +
107A HIS* 1.3 65.8 + - - +
109A LEU* 3.4 6.2 + - + +
110A ILE* 3.0 33.2 + - + +
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Residues in contact with HIS 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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90A ILE* 4.2 12.2 - - + +
103A VAL* 2.9 16.2 + - + +
104A ASP* 3.6 5.1 + - - +
106A PHE* 1.3 77.5 - - - +
108A GLN* 1.3 65.0 + - - +
110A ILE* 3.5 4.0 + - - +
111A LEU* 3.2 52.9 + - + +
121A MET* 3.5 27.9 - - + +
148A TYR* 3.3 62.0 + + + +
150A ILE* 4.9 1.7 - - + +
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Residues in contact with GLN 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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104A ASP* 2.8 32.3 + - - +
105A ARG* 3.8 9.2 - - - +
107A HIS* 1.3 78.2 + - - +
109A LEU* 1.3 60.4 + - + +
111A LEU* 3.4 6.1 + - - +
112A ARG* 3.0 35.8 + - + +
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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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72A GLU 5.6 0.7 - - - +
74A PHE* 3.8 39.7 - - + -
78A ARG* 4.6 9.9 - - - +
82A MET* 3.8 21.5 - - + -
105A ARG* 3.0 44.2 + - + +
106A PHE* 3.9 3.8 - - + +
108A GLN* 1.3 77.4 - - + +
110A ILE* 1.3 66.9 + - - +
112A ARG* 3.2 13.3 + - + -
113A VAL* 2.9 31.6 + - + +
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Residues in contact with ILE 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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19A VAL* 4.7 4.3 - - + -
82A MET* 3.8 30.1 - - + -
88A PHE* 3.7 53.4 - - + -
90A ILE* 4.0 21.5 - - + -
106A PHE 3.0 22.2 + - - +
107A HIS 3.9 3.1 - - - +
109A LEU* 1.3 76.0 - - - +
111A LEU* 1.3 58.6 + - - +
113A VAL* 3.9 1.0 - - - +
114A LYS* 2.9 43.4 + - + +
119A PHE* 4.5 6.1 - - + -
121A MET* 3.7 19.7 - - + -
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Residues in contact with LEU 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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107A HIS* 3.2 45.5 + - + +
108A GLN* 3.9 4.5 - - - +
110A ILE* 1.3 77.4 - - - +
112A ARG* 1.3 56.3 + - - +
114A LYS* 4.5 2.0 - - - -
115A ASP* 2.8 25.3 + - - -
116A ARG* 3.1 28.9 + - + +
117A GLU 3.5 18.8 - - - +
118A SER* 3.7 28.5 - - - +
119A PHE* 3.8 13.2 - - + +
121A MET* 4.2 9.4 - - + -
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Residues in contact with ARG 112 (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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83A ARG* 5.3 0.9 + - - -
108A GLN* 3.0 26.6 + - + +
109A LEU* 3.7 13.5 - - + +
111A LEU* 1.3 74.1 - - - +
113A VAL* 1.3 67.0 + - + +
115A ASP* 3.3 14.0 + - - +
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Residues in contact with VAL 113 (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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74A PHE* 3.9 28.5 - - + -
79A GLU* 3.9 7.2 - - + +
82A MET* 3.8 14.8 - - + -
83A ARG* 2.9 83.7 + - + +
109A LEU* 2.9 22.1 + - + +
110A ILE 3.9 2.9 - - - +
112A ARG* 1.3 79.9 - - + +
114A LYS* 1.3 60.7 + - - +
115A ASP* 3.5 1.7 + - - +
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Residues in contact with LYS 114 (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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82A MET 3.0 22.7 - - - +
83A ARG* 2.7 28.1 + - - +
84A THR 4.0 1.4 + - - -
85A GLY 2.8 27.2 + - - -
88A PHE* 4.2 2.7 - - - -
110A ILE* 2.9 27.2 + - + +
111A LEU* 4.0 4.0 - - - +
113A VAL* 1.3 76.3 - - - +
115A ASP* 1.3 69.8 + - - +
116A ARG* 3.7 25.8 - - + +
119A PHE* 3.4 35.3 - - + -
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Residues in contact with ASP 115 (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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111A LEU 2.8 11.7 + - - -
112A ARG* 3.3 9.3 + - - +
113A VAL 3.3 4.3 - - - +
114A LYS* 1.3 80.7 - - - +
116A ARG* 1.3 60.2 + - - +
117A GLU* 5.6 1.6 - - - +
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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