Contacts of the helix formed by residues 102 - 112 (chain A) in PDB entry 3QVN
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 SER 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 ASP* 2.8 42.7 + - - -
101A SER* 1.3 81.3 + - - +
103A ALA* 1.3 64.5 + - - +
104A LEU 4.0 1.7 + - - -
105A GLY 3.2 11.8 + - - -
106A LYS* 2.9 27.7 + - - +
201A GLU* 4.1 18.0 + - - +
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Residues in contact with ALA 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 SER 4.3 0.2 + - - -
102A SER* 1.3 73.9 - - - +
104A LEU* 1.3 63.6 + - - +
106A LYS* 3.3 8.2 + - - +
107A GLN* 3.0 23.2 + - - +
204A TYR* 4.0 22.5 - - + -
205A SER* 5.0 7.4 - - - +
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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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98A PRO* 4.7 2.7 - - + -
102A SER* 3.4 0.8 + - - -
103A ALA* 1.3 78.7 - - - +
105A GLY* 1.3 64.8 + - - +
107A GLN* 3.3 2.3 + - - +
108A ILE* 3.1 38.8 + - + +
137A ILE* 5.9 1.8 - - + -
147A LEU* 3.9 21.3 - - + -
166A ILE* 4.1 7.9 - - + -
197A TRP* 4.5 12.8 - - + -
200A ALA* 3.6 34.5 - - + +
201A GLU* 3.6 30.3 - - + +
204A TYR* 3.7 37.7 - - + -
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Residues in contact with GLY 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 PRO* 4.0 17.2 - - - +
99A ASP 3.3 21.8 - - - -
100A THR* 5.0 2.7 - - - -
102A SER* 3.2 9.2 + - - -
103A ALA 3.2 0.2 - - - -
104A LEU* 1.3 78.3 - - - +
106A LYS* 1.3 61.2 + - - +
108A ILE* 3.2 15.0 + - - +
109A VAL* 3.2 20.4 + - - +
115A VAL* 5.6 1.8 - - - +
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Residues in contact with LYS 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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99A ASP 4.3 0.6 + - - -
100A THR* 3.6 21.1 + - - +
101A SER* 3.8 23.5 + - - +
102A SER 2.9 20.7 + - - +
103A ALA* 3.8 6.7 - - - +
105A GLY* 1.3 73.6 - - - +
107A GLN* 1.3 56.4 + - - +
109A VAL* 3.4 8.2 + - - +
110A ALA* 3.1 28.6 + - - +
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Residues in contact with GLN 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 ALA 3.0 15.4 + - - +
104A LEU 3.5 5.6 - - - +
105A GLY 3.2 0.4 - - - -
106A LYS* 1.3 76.5 - - - +
108A ILE* 1.3 63.4 + - - +
110A ALA* 3.5 7.0 + - - +
111A GLN* 2.7 57.0 + - - +
144A GLY 5.2 2.8 + - - +
145A GLY 4.2 8.3 + - - +
146A ALA* 4.3 3.2 - - - +
147A LEU* 3.5 22.6 - - + +
204A TYR* 3.1 27.9 + - + +
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Residues in contact with ILE 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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98A PRO* 3.9 29.2 - - + -
104A LEU* 3.1 26.8 + - + +
105A GLY 3.2 5.8 + - - +
107A GLN* 1.3 77.1 - - - +
109A VAL* 1.3 58.7 + - + +
112A TYR* 2.8 32.2 + - + +
113A GLY 3.0 4.2 + - - -
114A SER 3.8 4.4 + - - +
115A VAL* 3.7 36.6 - - + +
118A LEU* 3.8 30.1 - - + -
137A ILE* 6.4 0.2 - - + -
147A LEU* 3.9 15.9 - - + -
197A TRP* 4.4 6.7 - - + -
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Residues in contact with VAL 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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100A THR* 5.5 12.8 - - + -
105A GLY 3.2 15.4 + - - +
106A LYS* 3.4 8.3 + - - +
107A GLN 3.3 0.2 - - - -
108A ILE* 1.3 77.9 - - + +
110A ALA* 1.3 62.8 + - - +
113A GLY* 3.0 42.2 + - - +
114A SER* 4.6 5.6 - - - -
115A VAL* 5.4 3.1 - - + +
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Residues in contact with ALA 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 LYS 3.1 16.5 + - - +
107A GLN* 3.9 11.2 - - - +
108A ILE 3.3 0.2 - - - -
109A VAL* 1.3 80.7 - - - +
111A GLN* 1.3 64.4 + - + +
113A GLY 4.8 0.3 + - - -
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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 GLN* 2.7 43.2 + - - +
110A ALA* 1.3 80.1 - - + +
112A TYR* 1.3 80.4 + - + +
113A GLY 3.7 0.2 - - - -
146A ALA* 3.4 10.8 - - - +
147A LEU* 2.8 47.4 + - - +
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Residues in contact with TYR 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 ILE* 2.8 27.4 + - + +
111A GLN* 1.3 95.2 + - + +
113A GLY* 1.3 56.6 + - - +
114A SER* 3.0 19.7 + - - +
117A ASN* 3.1 26.3 + - - +
118A LEU* 3.6 35.6 - - + +
121A ILE* 3.5 33.4 - - + -
147A LEU* 3.3 36.1 + - + +
148A ASP* 3.4 20.1 + - - -
149A VAL* 4.0 5.0 + - + +
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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