Contacts of the helix formed by residues 102 - 116 (chain A) in PDB entry 3O75
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 GLN 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A SER* 3.1 12.3 + - - +
100A ASP* 3.4 22.7 + - + +
101A ASP* 1.3 79.0 - - - +
103A PRO* 1.3 72.5 - - + +
104A ASP* 4.5 4.0 - - + +
105A SER* 3.2 16.5 + - - +
106A GLU* 3.0 21.8 + - - +
126A CYS* 3.6 3.3 - - - -
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Residues in contact with PRO 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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101A ASP 4.0 3.6 - - - +
102A GLN* 1.3 86.7 - - + +
104A ASP* 1.3 65.8 + - - +
106A GLU* 3.3 1.6 + - + +
107A ARG* 3.0 47.0 + - - +
126A CYS* 3.5 18.6 - - - +
127A LEU* 3.6 25.1 - - + -
128A PRO* 5.5 3.6 - - + -
188A ARG* 5.3 4.9 - - - +
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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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102A GLN* 3.2 4.0 - - + -
103A PRO* 1.3 81.4 - - - +
105A SER* 1.3 65.1 + - - +
107A ARG* 3.1 28.2 + - - +
108A GLN* 3.1 24.8 + - - +
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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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98A SER 5.1 0.2 - - - -
99A SER* 3.5 25.5 + - - -
102A GLN* 3.2 13.5 + - - +
104A ASP* 1.3 79.4 - - - +
106A GLU* 1.3 61.9 + - - +
108A GLN* 3.2 15.4 + - - +
109A LEU* 3.0 28.5 + - - +
88B ARG* 3.6 35.1 + - - -
93B GLN* 5.1 1.0 + - - +
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Residues in contact with GLU 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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67A ILE* 4.3 12.2 - - + +
99A SER* 4.0 16.6 + - - -
102A GLN 3.0 15.4 + - - +
103A PRO* 3.7 5.6 - - + +
104A ASP 3.2 0.4 - - - -
105A SER* 1.3 78.3 - - - +
107A ARG* 1.3 56.8 + - - +
109A LEU* 3.3 7.8 + - - +
110A GLN* 2.9 25.0 + - - +
123A VAL* 4.5 2.2 - - - -
124A ALA 4.8 0.5 - - - +
125A SER* 2.7 26.2 + - - -
126A CYS* 3.0 33.5 + - - -
127A LEU* 3.3 19.0 - - + +
134A TYR* 2.6 27.8 + - - +
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Residues in contact with ARG 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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103A PRO* 3.0 47.2 + - - +
104A ASP* 3.5 21.1 + - - +
106A GLU* 1.3 74.4 - - - +
108A GLN* 1.3 62.4 + - + +
110A GLN* 2.8 40.4 - - - +
111A GLN* 3.2 19.7 + - - +
127A LEU* 4.2 9.8 - - + +
128A PRO* 4.8 6.9 - - - +
131A ASP* 2.7 31.1 + - - +
133A SER* 5.8 1.1 - - - -
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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* 3.1 25.6 + - - +
105A SER* 3.2 14.2 + - - +
107A ARG* 1.3 76.8 - - + +
109A LEU* 1.3 60.9 + - - +
111A GLN* 3.3 23.3 + - - +
112A LEU 3.2 14.7 + - - -
88B ARG* 5.1 11.4 + - - +
93B GLN* 2.9 39.0 + - - +
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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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67A ILE* 3.7 29.4 - - + -
97A ALA* 3.9 26.5 - - + -
98A SER 3.2 34.5 - - - +
99A SER* 4.1 4.0 - - - +
105A SER* 3.0 18.4 + - - +
106A GLU* 3.6 6.7 - - - +
107A ARG 3.2 0.2 - - - -
108A GLN* 1.3 71.9 - - - +
110A GLN* 1.3 66.8 + - - +
112A LEU* 3.0 19.7 + - + +
113A PHE* 3.0 22.9 + - + -
88B ARG* 5.7 2.5 - - - +
93B GLN* 3.6 31.4 - - + +
94B LEU 5.3 0.9 - - - +
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Residues in contact with GLN 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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67A ILE* 4.3 5.3 - - - +
106A GLU 2.9 9.7 + - - +
107A ARG* 2.8 37.7 - - - +
109A LEU* 1.3 78.3 - - - +
111A GLN* 1.3 61.0 + - + +
113A PHE* 3.5 3.0 + - - +
114A ARG* 3.1 25.1 + - - +
121A LEU* 5.6 2.5 - - + +
127A LEU* 3.8 4.7 - - - +
133A SER* 2.6 40.2 + - - -
134A TYR* 3.2 38.2 + - + +
137A LEU* 3.4 26.4 - - + +
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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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107A ARG* 3.2 23.3 + - - +
108A GLN* 3.5 22.5 - - - +
109A LEU 3.2 0.2 - - - -
110A GLN* 1.3 77.2 - - + +
112A LEU* 1.3 59.8 + - - +
114A ARG* 3.0 44.7 + - - +
115A ALA* 3.2 12.1 + - - +
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Residues in contact with LEU 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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108A GLN 3.2 9.6 + - - +
109A LEU* 3.0 17.3 + - + +
111A GLN* 1.3 78.0 - - - +
113A PHE* 1.3 60.2 + - + +
115A ALA* 3.0 6.8 + - + +
116A ARG* 2.8 52.1 + - - +
63B THR* 3.6 23.1 - - + -
93B GLN* 3.6 37.7 - - + +
94B LEU 5.3 0.4 - - - +
95B LEU* 3.7 33.9 - - + -
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Residues in contact with PHE 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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65A GLY* 3.4 20.6 - - - -
66A PHE 4.0 5.8 - - - -
67A ILE* 3.7 29.2 - - + -
95A LEU* 3.4 37.2 - - + -
97A ALA* 3.7 29.8 - - + -
109A LEU* 3.0 29.3 + - + +
110A GLN 4.4 2.2 - - - +
112A LEU* 1.3 79.1 - - + +
114A ARG* 1.3 56.6 + - - +
116A ARG* 3.8 5.8 + - + +
117A ARG 3.2 15.6 + - - -
118A CYS* 3.2 29.3 + - + +
121A LEU* 3.9 20.0 - - + -
142A LEU* 5.2 5.9 - - + +
95B LEU* 4.1 15.3 - - + -
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Residues in contact with ARG 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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110A GLN* 3.1 19.9 + - - +
111A GLN* 3.0 46.1 + - - +
113A PHE* 1.3 75.7 - - - +
115A ALA* 1.3 60.0 + - + +
117A ARG* 3.0 35.9 + - - +
136A GLU* 5.0 5.2 + - - -
137A LEU* 3.4 31.7 - - + +
140A LYS* 4.0 24.0 - - - +
142A LEU* 4.9 10.7 - - + +
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Residues in contact with ALA 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 GLN 3.2 14.4 + - - +
112A LEU* 3.0 12.0 + - + +
114A ARG* 1.3 75.2 - - + +
116A ARG* 1.3 75.1 + - - +
117A ARG* 2.8 12.9 + - - +
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Residues in contact with ARG 116 (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 THR* 4.4 1.6 - - - +
95A LEU* 4.2 10.5 - - + -
112A LEU* 2.8 37.1 + - - +
113A PHE* 3.8 9.2 - - + +
115A ALA* 1.3 90.6 + - - +
117A ARG* 1.3 68.0 + - - +
118A CYS* 3.2 9.7 + - - -
61B THR* 4.3 18.8 + - - +
63B THR* 3.4 25.1 + - - +
95B LEU* 3.6 21.0 - - + +
116B ARG* 3.4 77.4 + - - +
118B CYS* 4.6 1.0 - - - -
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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