Contacts of the helix formed by residues 63 - 75 (chain A) in PDB entry 2QQ6
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 ASP 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A ASP* 3.6 18.1 + - - +
61A PRO 3.0 4.3 + - - -
62A ARG* 1.3 80.6 - - - +
64A VAL* 1.3 58.7 + - - +
65A GLU 3.5 2.2 - - - -
66A ARG* 3.5 41.3 + - + +
67A LEU* 3.1 28.9 + - - +
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Residues in contact with VAL 64 (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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61A PRO 3.5 14.8 + - - +
62A ARG 3.5 7.8 + - - +
63A ASP* 1.3 71.5 - - - +
65A GLU* 1.3 57.9 + - - +
67A LEU* 2.9 9.7 + - - +
68A TYR* 2.7 33.8 + - - +
93A GLU* 4.0 16.8 - - + +
96A LEU* 4.1 15.7 - - + +
97A TRP* 3.3 69.1 - - + +
100A ALA* 4.6 5.4 - - + -
297A ALA* 5.1 0.7 - - + -
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Residues in contact with GLU 65 (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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63A ASP 3.5 0.6 - - - -
64A VAL* 1.3 83.2 - - + +
66A ARG* 1.3 62.9 + - - +
68A TYR* 3.1 11.0 + - + +
69A GLU* 3.1 27.9 + - + +
97A TRP* 4.8 8.5 - - + -
297A ALA* 4.3 21.7 - - + +
301A ARG* 4.1 27.5 + - - +
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Residues in contact with ARG 66 (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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59A GLU* 3.5 30.3 + - - -
60A ASP* 4.3 8.3 + - - +
63A ASP* 3.5 38.0 + - + +
64A VAL 3.2 0.6 - - - -
65A GLU* 1.3 79.5 - - - +
67A LEU* 1.3 83.4 + - - +
69A GLU* 3.4 7.3 + - - +
70A LYS* 3.1 27.1 + - - +
182B TRP* 3.7 38.9 - - + +
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Residues in contact with LEU 67 (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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6A ILE* 4.5 2.7 - - + -
56A LEU* 4.3 12.8 - - + -
59A GLU* 4.0 25.1 - - + +
60A ASP 3.6 19.1 - - - +
61A PRO* 4.2 12.6 - - + +
63A ASP 3.1 15.7 + - - +
64A VAL 2.9 8.6 + - - +
66A ARG* 1.3 107.6 - - - +
68A TYR* 1.3 62.3 + - - +
70A LYS* 3.3 11.4 - - + +
71A MSE 3.3 29.4 + - - +
96A LEU* 3.7 31.0 - - + -
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Residues in contact with TYR 68 (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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64A VAL 2.7 15.9 + - - +
65A GLU* 3.4 16.4 - - + +
66A ARG 3.1 0.2 - - - -
67A LEU* 1.3 70.6 - - - +
69A GLU* 1.3 68.6 + - + +
70A LYS 2.9 4.5 + - - -
71A MSE 3.2 13.2 + - + +
72A ARG* 2.8 56.1 + - + +
86A ILE* 4.4 7.6 - - - +
89A LEU* 4.0 30.0 - - + +
93A GLU* 4.4 25.4 - - + +
96A LEU* 6.0 0.2 - - - -
270A THR* 5.3 1.6 - - - +
271A ARG* 4.4 2.7 - - - -
293A CYS 4.3 2.1 + - - -
294A GLY* 3.6 36.4 - - - -
297A ALA* 5.6 5.6 - - + -
298A GLU* 3.7 30.0 + - + -
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Residues in contact with GLU 69 (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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65A GLU* 3.1 17.4 + - + +
66A ARG* 3.9 5.8 - - - +
68A TYR* 1.3 82.6 - - + +
70A LYS* 1.3 56.2 + - - +
72A ARG* 3.1 37.9 + - - -
73A ARG* 2.8 73.1 + - - +
271A ARG* 3.6 25.2 + - - +
301A ARG* 5.8 3.8 - - - +
182B TRP* 4.1 15.5 - - + -
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Residues in contact with LYS 70 (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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55A GLN* 3.1 53.4 + - + +
56A LEU* 6.2 0.7 - - + -
59A GLU* 3.5 24.1 + - - +
66A ARG* 3.1 19.4 + - - +
67A LEU* 3.3 19.7 - - + +
68A TYR 2.9 1.4 - - - -
69A GLU* 1.3 74.9 - - - +
71A MSE 1.3 67.7 + - + +
73A ARG* 3.9 1.9 - - - +
74A TRP* 3.1 24.3 + - - +
181B PHE* 5.8 5.1 - - + -
182B TRP* 3.9 19.8 - - + -
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Residues in contact with MSE 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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52A MSE 3.2 36.3 - - + -
55A GLN* 4.7 7.2 - - + -
56A LEU* 4.0 17.5 - - + -
67A LEU 3.4 16.8 - - - +
68A TYR* 3.2 16.0 + - + +
70A LYS* 1.3 77.5 - - + +
72A ARG* 1.3 60.0 + - - +
74A TRP* 3.3 11.6 + - - +
75A ASN* 2.4 30.8 + - - -
89A LEU* 3.6 29.6 - - + +
92A ILE* 3.5 37.2 - - + -
93A GLU* 4.4 5.8 - - - +
96A LEU* 4.4 13.5 - - + -
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Residues in contact with ARG 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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68A TYR* 2.8 45.1 + - + +
69A GLU* 3.1 39.8 + - - +
71A MSE 1.3 79.1 - - - +
73A ARG* 1.3 76.2 + - - +
75A ASN* 3.2 14.9 + - - +
76A ILE* 3.7 7.1 + - - -
80A GLY* 4.3 22.3 + - - +
81A GLN* 6.3 0.8 - - - +
86A ILE* 5.7 1.3 - - + -
89A LEU* 3.9 15.7 - - + +
270A THR* 4.5 12.5 - - - +
271A ARG* 4.4 6.7 - - - +
272A PHE* 3.6 13.2 - - - -
298A GLU* 5.0 0.9 - - - -
246B GLU* 3.2 43.9 + - - +
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Residues in contact with ARG 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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69A GLU* 2.8 57.2 + - - +
70A LYS* 4.2 2.2 - - - +
72A ARG* 1.3 88.8 - - - +
74A TRP* 1.3 56.1 + - - +
75A ASN 3.2 0.2 - - - -
76A ILE* 2.9 32.7 - - - +
271A ARG* 5.6 0.6 - - - +
134B ALA* 4.6 2.8 - - - +
136B HIS* 5.9 0.2 + - - -
181B PHE* 4.2 12.3 + - + -
182B TRP* 2.7 56.5 + - + +
183B ASN 5.1 0.6 + - - -
218B ARG* 5.0 3.4 + - - +
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Residues in contact with TRP 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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51A ASN* 5.1 7.6 + - - -
52A MSE 3.1 30.3 - - + +
55A GLN* 3.4 33.4 - - + +
70A LYS 3.1 17.7 + - - +
71A MSE 3.5 8.1 - - - +
72A ARG 3.1 0.4 - - - -
73A ARG* 1.3 77.4 - - - +
75A ASN* 1.3 64.0 + - - +
76A ILE* 3.4 1.8 + - - +
77A PHE 4.9 0.3 + - - -
78A THR* 4.3 5.4 + - - +
132B ASP* 3.1 36.1 - - - -
133B ALA* 3.4 26.9 - - + +
134B ALA* 3.5 29.5 + - + +
136B HIS* 4.8 6.3 - + - -
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Residues in contact with ASN 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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48A ILE* 5.6 2.3 - - - +
51A ASN* 5.6 1.6 - - - +
52A MSE 3.5 28.0 - - - +
71A MSE 2.4 31.7 + - - +
72A ARG* 3.2 4.9 + - - +
73A ARG 3.2 0.4 - - - -
74A TRP* 1.3 84.4 - - - +
76A ILE* 1.3 60.0 + - - +
77A PHE 3.2 2.9 - - - -
78A THR* 2.9 29.5 + - - +
80A GLY* 2.6 44.6 + - - +
85A VAL* 3.7 23.4 - - + +
89A LEU* 4.7 2.6 - - - +
40B ALA* 4.9 5.9 - - - +
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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