Contacts of the helix formed by residues 70 - 78 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66D ASN 3.7 3.7 + - - -
67D VAL* 3.2 11.5 + - - -
68D ALA 3.0 2.4 - - - -
69D LEU* 1.3 81.7 - - - +
71D TYR* 1.3 62.4 + - - +
72D PRO 3.5 0.4 - - - -
73D VAL* 3.2 12.7 + - - +
74D SER* 3.0 27.0 + - - -
275D GLN* 6.0 1.1 - - - -
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Residues in contact with TYR 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.4 13.4 - - + +
118C GLN* 6.1 0.4 - - - -
198C TRP* 3.4 13.7 - + + -
201C ARG* 3.0 45.1 - - - +
202C LEU* 3.7 13.9 - - + -
205C GLU* 2.5 25.0 + - - -
67D VAL* 3.8 20.9 + - + +
68D ALA* 3.0 32.9 - - - -
70D GLY* 1.3 72.7 - - - +
72D PRO* 1.3 66.2 - - + +
73D VAL 3.0 1.6 - - - -
74D SER* 2.7 25.5 + - - -
75D ALA* 2.8 13.2 + - - +
800D CIT 3.5 20.4 + - - -
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Residues in contact with PRO 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C LEU* 3.3 15.5 - - + -
194C VAL* 5.1 6.5 - - + -
198C TRP* 3.6 31.4 - - + +
38D ILE* 5.8 0.2 - - + -
39D GLY* 4.6 3.4 - - - -
42D PHE* 3.3 47.8 - - + -
68D ALA 4.0 2.5 - - - +
69D LEU 4.3 1.8 - - - -
70D GLY 3.8 2.9 - - - +
71D TYR* 1.3 95.6 - - + +
73D VAL* 1.3 50.1 + - - +
75D ALA* 3.9 0.4 - - + -
76D THR* 2.5 43.9 + - + +
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Residues in contact with VAL 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D GLY 4.2 4.5 - - - +
42D PHE* 4.2 2.9 - - + -
43D LEU* 3.9 39.9 - - + +
69D LEU 3.2 26.7 - - - +
70D GLY* 3.4 11.7 - - - +
71D TYR 3.0 0.2 - - - -
72D PRO* 1.3 75.2 - - - +
74D SER* 1.3 57.6 + - - +
76D THR* 3.6 4.0 - - - -
77D PHE* 3.2 50.6 + - + +
78D ASN* 3.8 3.4 + - - -
271D ARG* 4.0 19.1 + - - +
275D GLN* 4.6 6.7 - - - +
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Residues in contact with SER 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PHE* 3.5 36.6 - - - +
70D GLY 3.0 11.4 + - - -
71D TYR* 2.7 13.5 + - - -
73D VAL* 1.3 77.8 - - - +
75D ALA* 1.3 61.1 + - - -
76D THR 3.2 1.5 + - - -
78D ASN* 3.1 45.0 + - - +
79D ILE* 3.8 4.9 - - - +
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Residues in contact with ALA 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 3.6 30.3 - - + +
112C LEU* 4.4 1.7 - - - +
113C LEU* 3.6 49.8 - - + +
117C PHE* 4.7 6.5 - - + -
71D TYR 2.8 9.0 + - - +
72D PRO* 4.1 2.2 - - + +
74D SER* 1.3 72.8 - - - +
76D THR* 1.3 58.9 + - + +
79D ILE* 3.4 24.1 - - - +
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Residues in contact with THR 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C VAL* 4.4 13.0 - - + -
194C VAL* 5.9 2.2 - - + -
35D PHE* 3.5 43.5 - - + +
36D LEU* 4.1 5.2 - - - +
38D ILE* 4.9 6.7 - - + -
39D GLY* 3.4 19.1 - - - +
72D PRO* 2.5 24.5 + - + +
73D VAL* 3.6 3.8 + - - -
75D ALA* 1.3 81.4 - - + +
77D PHE* 1.3 74.0 + - - +
78D ASN 3.2 1.1 - - - -
79D ILE* 3.1 13.7 + - - +
80D MET* 3.4 12.1 + - - +
83D ILE* 4.9 3.9 - - - +
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Residues in contact with PHE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 4.0 25.1 - - + -
39D GLY* 3.8 1.6 - - - -
40D SER* 2.9 47.3 - - - -
43D LEU* 4.8 2.0 - - + -
73D VAL* 3.2 27.0 + - + +
76D THR* 1.3 91.4 + - - +
78D ASN* 1.3 59.2 + - - +
79D ILE 3.1 1.3 + - - -
80D MET* 3.2 25.7 - - - +
142D GLY* 3.7 6.1 - - - -
143D SER 4.0 1.0 + - - -
267D MET* 3.3 35.9 - - + -
268D ASP* 3.9 6.7 - - - +
271D ARG* 3.6 35.9 - - - +
377D GLY 4.4 4.3 - - - -
378D ALA* 4.7 2.9 - - - -
379D ALA* 4.3 6.1 - - + -
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Residues in contact with ASN 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C PHE* 5.2 1.1 - - + -
134C GLY* 6.2 1.8 - - - -
74D SER* 3.1 39.5 + - - +
76D THR 3.2 1.2 - - - -
77D PHE* 1.3 75.0 - - - +
79D ILE* 1.3 68.9 + - + +
138D ALA* 3.6 24.5 - - + +
139D ALA* 5.8 0.7 - - - -
141D MET* 3.3 5.5 - - - +
142D GLY* 3.1 25.0 + - - -
268D ASP* 4.8 2.8 - - - +
271D ARG* 3.5 31.6 + - - +
272D ILE* 6.0 0.9 - - - +
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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