Contacts of the helix formed by residues 70 - 77 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A SER* 5.7 0.4 - - - -
66A ASN 3.6 7.5 + - - -
67A VAL* 3.3 11.5 + - - -
68A ALA 2.9 2.2 - - - -
69A LEU* 1.3 79.0 - - - +
71A TYR* 1.3 62.9 + - - +
72A PRO 3.8 0.2 - - - -
73A VAL* 3.9 12.2 - - - +
74A SER* 3.2 26.2 + - - -
275A GLN* 5.1 8.7 - - - -
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Residues in contact with TYR 71 (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 VAL* 3.8 23.0 - - + +
68A ALA* 2.8 22.4 + - + +
70A GLY* 1.3 79.3 - - - +
72A PRO* 1.4 74.4 - - + +
73A VAL 3.1 0.9 - - - -
74A SER* 3.0 17.2 + - - -
75A ALA* 3.2 9.2 + - - +
113B LEU* 3.5 13.9 - - + +
198B TRP* 3.9 3.4 - - + -
201B ARG* 3.0 47.3 + - - +
202B LEU* 3.7 27.6 - - + -
205B GLU* 3.1 25.3 + - + -
800B CIT 4.0 13.7 + - - -
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Residues in contact with PRO 72 (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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38A ILE* 5.5 2.2 - - + -
39A GLY* 4.6 4.0 - - - -
42A PHE* 3.3 57.2 - - + -
68A ALA 3.3 9.0 - - - +
69A LEU 4.2 4.0 - - - -
70A GLY 4.1 0.4 - - - -
71A TYR* 1.4 95.9 - - + +
73A VAL* 1.3 59.7 + - - +
75A ALA* 3.3 2.6 + - + +
76A THR* 2.9 32.7 + - + +
113B LEU* 3.8 13.7 - - + -
194B VAL* 5.6 3.1 - - + -
198B TRP* 3.6 16.4 - - + +
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Residues in contact with VAL 73 (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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39A GLY* 3.7 20.2 - - - +
42A PHE* 4.3 1.1 - - + -
43A LEU* 3.8 18.6 - - + +
69A LEU 3.4 22.9 - - - +
70A GLY* 3.9 11.0 - - - +
71A TYR 3.1 1.0 - - - -
72A PRO* 1.3 77.0 - - - +
74A SER* 1.3 56.4 + - - +
76A THR* 3.7 4.9 - - - -
77A PHE* 3.1 49.5 + - + +
78A ASN* 3.7 1.1 + - - +
271A ARG* 3.8 25.8 - - - +
275A GLN* 4.0 11.2 - - - +
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Residues in contact with SER 74 (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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70A GLY 3.2 13.0 + - - -
71A TYR* 3.0 13.3 + - - -
73A VAL* 1.3 78.1 - - - +
75A ALA* 1.3 61.8 + - - +
76A THR 3.5 0.2 + - - -
78A ASN* 3.3 41.6 + - - +
79A ILE* 3.7 7.8 - - - +
117B PHE* 4.1 29.8 - - - +
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Residues in contact with ALA 75 (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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71A TYR 3.2 10.9 + - - +
72A PRO* 3.3 5.4 + - + +
73A VAL 3.3 0.2 - - - -
74A SER* 1.3 78.1 - - - +
76A THR* 1.3 59.1 + - + +
79A ILE* 3.6 20.7 - - - +
109B VAL* 3.7 28.4 - - + +
112B LEU* 4.4 1.2 - - - +
113B LEU* 3.6 45.1 - - + +
117B PHE* 4.8 5.4 - - + -
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Residues in contact with THR 76 (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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35A PHE* 3.6 50.0 - - + +
36A LEU* 4.2 6.9 - - - +
38A ILE* 4.9 6.7 - - + -
39A GLY* 3.4 18.8 - - - +
72A PRO* 2.9 19.0 + - + +
73A VAL 3.3 3.1 + - - -
75A ALA* 1.3 82.0 - - + +
77A PHE* 1.3 77.4 + - - +
78A ASN 3.3 0.9 - - - -
79A ILE* 2.8 22.9 + - - +
80A MET* 3.4 3.3 + - - +
83A ILE* 5.1 2.4 - - - +
109B VAL* 4.6 7.6 - - + -
194B VAL* 5.7 1.8 - - + -
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Residues in contact with PHE 77 (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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36A LEU* 4.1 22.4 - - + +
39A GLY 3.8 3.4 - - - -
40A SER* 3.1 44.4 - - - -
43A LEU* 5.0 2.5 - - + -
73A VAL* 3.1 27.3 + - + +
76A THR* 1.3 88.9 + - - +
78A ASN* 1.3 60.4 + - - +
79A ILE 3.1 5.0 + - - -
80A MET* 3.3 24.9 + - - +
142A GLY* 3.8 5.4 - - - -
143A SER 4.3 0.9 + - - -
267A MET* 4.2 18.8 - - - -
268A ASP* 3.8 9.7 - - - +
271A ARG* 3.5 41.7 - - + +
377A GLY 3.9 13.0 - - - -
378A ALA* 4.7 2.0 - - - -
379A ALA* 4.0 10.1 - - + -
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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