Contacts of the helix formed by residues 103 - 112 (chain A) in PDB entry 3Q72
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A GLY 3.3 1.0 - - - -
102A VAL* 1.3 81.3 - - - +
104A LYS* 1.3 64.7 + - - +
106A ALA* 3.3 1.7 + - - +
107A LEU* 3.0 32.8 + - - +
168A VAL* 5.0 0.4 - - - -
203A ASN* 3.6 11.3 + - - -
256A GNP 3.0 34.6 + - - -
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Residues in contact with LYS 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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96A LEU* 3.4 30.7 - - + +
97A LEU* 3.6 32.5 - - - +
98A GLY* 3.2 11.3 + - - +
99A ALA 2.5 31.7 + - - -
102A VAL* 3.7 11.1 - - + +
103A GLY* 1.3 77.2 - - - +
105A SER* 1.3 60.9 + - - +
107A LEU* 3.6 2.8 + - - +
108A ALA 3.3 15.2 + - - -
144A ASP* 3.7 15.3 - - - +
146A TRP* 3.9 18.6 - - - -
168A VAL* 4.2 13.9 - - + +
256A GNP 2.8 42.6 + - - +
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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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104A LYS* 1.3 73.0 - - - +
106A ALA* 1.3 57.2 + - - +
108A ALA* 3.2 3.4 + - - +
109A ARG* 2.8 59.2 + - - +
125A HIS* 3.7 12.8 + - - -
144A ASP* 2.6 23.2 + - - -
256A GNP 3.2 9.3 + - - -
257A MG 2.3 30.3 - - - -
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Residues in contact with ALA 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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103A GLY 3.3 5.4 + - - +
105A SER* 1.3 76.7 - - - +
107A LEU* 1.3 62.3 + - - +
109A ARG* 3.7 20.1 - - - +
110A ILE* 3.0 32.4 + - + +
234A ALA* 3.7 18.8 - - + -
256A GNP 3.0 33.4 + - + +
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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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96A LEU* 5.3 3.6 - - + -
103A GLY 3.0 19.9 + - - +
104A LYS* 3.8 4.5 - - - +
106A ALA* 1.3 76.9 - - - +
108A ALA* 1.3 62.4 + - - +
110A ILE* 3.4 4.6 + - - +
111A PHE* 3.1 24.1 + - - +
166A VAL* 5.9 0.4 - - + -
168A VAL* 4.0 35.2 - - + -
201A VAL* 4.5 6.7 - - + -
203A ASN* 3.9 12.1 - - - +
232A THR* 3.7 26.2 - - + +
234A ALA* 4.0 7.0 - - + -
240A VAL* 3.6 35.2 - - + +
243A LEU* 4.7 9.2 - - + -
244A PHE* 4.1 10.9 - - + -
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Residues in contact with ALA 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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96A LEU* 3.4 28.2 - - + +
104A LYS 3.3 6.7 + - - +
105A SER* 3.2 6.6 + - - +
107A LEU* 1.3 78.6 - - - +
109A ARG* 1.3 59.6 + - - +
111A PHE* 3.4 6.4 + - - +
112A GLY* 2.9 27.2 + - - -
127A TYR* 3.8 32.5 - - + +
142A VAL* 4.2 9.4 - - + -
144A ASP* 4.6 2.5 - - + -
244A PHE* 4.9 0.9 - - - -
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Residues in contact with ARG 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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105A SER* 2.8 45.2 + - - +
106A ALA* 3.7 22.6 - - - +
108A ALA* 1.3 71.2 - - - +
110A ILE* 1.3 60.0 + - + +
112A GLY 2.7 22.0 - - - +
125A HIS* 4.4 8.1 - - - -
127A TYR* 3.1 37.7 - - + +
256A GNP 5.1 5.7 + - - -
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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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106A ALA* 3.0 24.5 + - + +
107A LEU* 3.6 4.5 - - - +
109A ARG* 1.3 73.2 - - + +
111A PHE* 1.3 67.5 + - - +
112A GLY 3.1 9.2 + - - +
129A ARG* 5.2 1.0 + - - -
234A ALA* 3.1 43.3 - - + +
237A HIS* 3.7 36.8 - - + +
240A VAL* 3.9 24.9 - - + -
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Residues in contact with PHE 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 LEU 3.1 14.9 + - - +
108A ALA 3.7 3.6 - - - +
110A ILE* 1.3 80.5 - - - +
112A GLY* 1.3 62.0 + - - +
127A TYR* 4.4 4.9 - - + -
129A ARG* 3.1 66.7 + - + +
131A ILE* 3.8 15.3 - - + -
140A LEU* 3.4 32.1 - - + -
142A VAL* 3.4 32.1 - - + -
240A VAL* 4.3 5.3 - - + +
241A GLN* 4.4 8.1 - - - -
244A PHE* 3.4 43.7 - + + -
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Residues in contact with GLY 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 ALA 2.9 15.9 + - - -
109A ARG 2.7 21.6 - - - +
110A ILE 3.1 7.5 - - - +
111A PHE* 1.3 79.5 - - - +
113A GLY* 1.3 61.1 + - - -
127A TYR* 4.3 9.0 - - - -
128A ASP 4.2 6.1 - - - -
129A ARG* 4.8 0.7 - - - -
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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