Contacts of the helix formed by residues 70 - 78 (chain B) in PDB entry 3QNQ
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 70 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B ASN 3.8 3.4 + - - -
67B VAL* 3.0 12.7 + - - -
68B ALA 2.8 1.8 + - - -
69B LEU* 1.3 79.0 - - - +
71B TYR* 1.3 65.8 + - - +
72B PRO 3.7 1.1 - - - -
73B VAL* 3.5 12.0 + - - +
74B SER* 3.2 20.1 + - - -
275B GLN* 5.6 4.0 - - - -
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Residues in contact with TYR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU* 3.4 8.6 - - + +
118A GLN* 5.5 7.8 + - - -
198A TRP* 3.6 11.4 - + + +
201A ARG* 3.0 46.5 + - - +
202A LEU* 3.4 32.5 - - + -
205A GLU* 2.6 24.9 + - - -
67B VAL* 4.1 20.6 - - + +
68B ALA* 2.8 19.1 + - - +
70B GLY* 1.3 74.5 - - - +
72B PRO* 1.3 69.3 - - + +
73B VAL 3.1 1.6 - - - -
74B SER* 2.8 25.7 + - - -
75B ALA 3.1 9.2 + - - -
443B CIT 3.9 15.2 + - - -
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Residues in contact with PRO 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU* 3.4 16.4 - - + -
194A VAL* 5.5 5.6 - - + -
198A TRP* 3.4 24.9 - - + +
38B ILE* 5.5 1.1 - - + -
39B GLY* 4.7 3.8 - - - -
42B PHE* 3.4 48.0 - - + -
68B ALA 3.6 2.5 - - - +
69B LEU 4.3 6.1 - - - -
70B GLY 3.9 0.7 - - - -
71B TYR* 1.3 95.7 - - + +
73B VAL* 1.3 56.4 + - - +
75B ALA* 3.3 1.3 + - + -
76B THR* 2.8 38.6 + - + +
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLY 3.7 17.0 - - - +
42B PHE* 4.3 1.8 - - + -
43B LEU* 3.9 26.0 - - + +
69B LEU 3.6 23.8 - - - +
70B GLY* 3.6 11.0 - - - +
71B TYR 3.1 0.4 - - - -
72B PRO* 1.3 72.4 - - - +
74B SER* 1.3 62.1 + - - +
76B THR* 3.7 5.4 - - - -
77B PHE* 3.0 54.5 + - + +
78B ASN* 3.6 3.3 + - - -
271B ARG* 4.0 22.2 - - - +
275B GLN* 4.6 6.7 - - - +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PHE* 3.5 37.4 - - - +
201A ARG* 6.3 0.2 - - - -
70B GLY 3.2 9.6 + - - -
71B TYR* 2.8 14.7 + - - -
73B VAL* 1.3 79.8 - - - +
75B ALA* 1.3 61.7 + - - +
76B THR 3.2 1.2 + - - -
78B ASN* 3.2 42.4 + - - +
79B ILE* 3.9 6.8 - - - +
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Residues in contact with ALA 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 3.7 23.5 - - + +
112A LEU* 4.3 1.1 - - + +
113A LEU* 3.4 49.6 - - + +
117A PHE* 4.8 2.5 - - + -
71B TYR 3.1 2.6 + - - +
72B PRO* 3.3 4.4 + - + +
74B SER* 1.3 78.1 - - - +
76B THR* 1.3 60.9 + - + +
79B ILE* 3.6 31.2 - - - +
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Residues in contact with THR 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 4.4 14.1 - - + -
194A VAL* 5.9 2.7 - - + -
35B PHE* 3.9 39.8 - - + +
36B LEU* 4.0 4.6 - - - +
38B ILE* 5.1 6.1 - - + -
39B GLY* 3.5 18.4 - - - +
72B PRO* 2.8 21.6 + - + +
73B VAL* 3.5 4.3 + - - -
75B ALA* 1.3 84.1 - - + +
77B PHE* 1.3 72.4 + - - +
78B ASN 3.4 1.3 - - - -
79B ILE* 3.4 3.3 + - - +
80B MET* 3.0 29.5 + - - +
83B ILE* 5.2 3.1 - - - +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B LEU* 3.7 24.7 - - + -
39B GLY 4.1 10.1 - - - -
40B SER* 3.5 27.1 - - - -
43B LEU* 5.1 4.0 - - + -
73B VAL* 3.0 29.9 + - + +
76B THR* 1.3 88.1 + - - +
78B ASN* 1.3 57.5 + - - +
79B ILE 3.2 3.4 + - - -
80B MET* 3.4 23.1 - - - +
142B GLY* 3.8 6.6 - - - -
267B MET* 3.5 30.7 - - + -
268B ASP* 3.8 14.0 - - - +
271B ARG* 3.6 33.9 - - - +
377B GLY 4.0 7.2 - - - -
378B ALA* 4.7 1.1 - - - -
379B ALA* 3.9 14.8 - - + -
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Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A PHE* 5.4 0.9 - - + -
73B VAL 4.4 0.2 - - - -
74B SER* 3.2 39.3 + - - +
76B THR 3.4 0.6 - - - -
77B PHE* 1.3 75.0 - - - +
79B ILE* 1.3 64.2 + - + +
138B ALA* 3.5 24.6 - - + +
139B ALA* 5.9 0.2 - - - -
141B MET* 3.1 20.8 - - - +
142B GLY* 3.4 13.8 + - - -
268B ASP* 4.9 0.9 - - - +
271B ARG* 3.4 32.3 + - - +
272B ILE* 5.5 2.9 - - - +
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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