Contacts of the helix formed by residues 61 - 76 (chain A) in PDB entry 2FQ6
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 THR 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLN* 2.9 40.8 + - + +
31A ALA* 4.0 31.6 - - + +
34A LEU* 4.5 7.9 - - + -
54A LEU* 3.7 7.2 - - - -
57A GLY* 4.6 2.2 - - - -
60A GLY* 1.3 78.2 - - - +
62A LEU* 1.3 66.1 + - - +
63A THR* 3.3 10.2 + - - -
64A HIS* 2.8 23.8 + - + +
65A PHE* 2.9 30.4 + - - -
246A ALA* 5.2 0.4 - - + -
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Residues in contact with LEU 62 (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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18A LYS* 4.1 9.6 - - + +
19A TYR* 3.8 28.6 - - + +
21A LEU* 4.0 26.7 - - + -
26A SER* 5.7 0.7 - - - -
27A VAL* 4.0 18.4 - - + -
29A GLN* 3.1 25.0 + - - +
52A GLY 6.0 0.2 - - - +
54A LEU* 3.8 15.1 - - + +
61A THR* 1.3 75.3 - - - +
63A THR* 1.3 57.2 + - - +
65A PHE* 3.4 12.5 + - + +
66A SER* 3.0 29.8 + - - -
21B LEU* 4.9 10.1 - - + +
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Residues in contact with THR 63 (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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26A SER* 4.1 7.9 + - - +
27A VAL 2.7 27.8 + - - +
28A ILE* 4.5 1.3 - - - -
29A GLN* 2.9 23.2 + - - +
61A THR* 3.1 7.5 - - - -
62A LEU* 1.3 79.5 - - - +
64A HIS* 1.3 61.9 + - - +
66A SER* 3.6 2.6 + - - -
67A LEU* 3.2 21.0 + - - +
246A ALA* 3.4 31.6 - - - +
249A ALA* 4.2 2.1 - - + +
250A TYR* 3.7 22.9 - - + +
253A SER* 4.9 0.9 + - - -
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Residues in contact with HIS 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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57A GLY 4.6 3.0 + - - -
59A ARG 5.0 0.4 - - - +
60A GLY* 3.3 17.9 - - - -
61A THR* 2.8 45.1 + - - +
63A THR* 1.3 73.0 - - - +
65A PHE* 1.3 62.7 + - - +
67A LEU* 3.2 3.3 + - - +
68A GLN* 2.9 41.6 + - - +
82A LEU* 4.1 20.0 - - + +
243A MET* 4.6 7.4 - - + +
244A VAL* 2.7 31.3 + - - +
245A ASP* 3.6 2.7 - - - -
246A ALA* 3.5 29.8 + - - +
249A ALA* 4.2 10.6 - - - +
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Residues in contact with PHE 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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19A TYR* 3.4 29.4 + + + +
49A ARG 5.9 2.2 - - - -
52A GLY* 3.4 46.9 - - - -
53A GLU 4.1 10.8 - - - -
54A LEU* 3.8 25.4 - - + -
55A PHE 5.4 0.2 - - - -
59A ARG* 4.0 13.7 - - + -
60A GLY 3.5 27.1 - - - -
61A THR 2.9 20.7 + - - +
62A LEU* 3.8 9.9 - - + +
64A HIS* 1.3 75.6 - - + +
66A SER* 1.3 58.1 + - - +
68A GLN* 3.6 19.3 - - - +
69A GLN* 2.9 31.4 + - - +
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Residues in contact with SER 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLY* 2.6 35.4 + - - -
15A ARG* 4.8 0.9 - - - +
19A TYR* 3.8 22.9 - - - +
26A SER* 3.6 21.7 + - - -
62A LEU 3.0 18.0 + - - -
63A THR 3.7 5.2 - - - -
65A PHE* 1.3 78.0 - - - +
67A LEU* 1.3 62.3 + - - +
69A GLN* 3.5 0.3 + - - +
70A ALA* 3.1 18.2 + - - +
253A SER* 4.3 5.4 + - - -
257A ARG* 5.4 2.9 + - - -
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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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63A THR 3.2 9.7 + - - +
64A HIS 3.2 7.4 + - - +
66A SER* 1.3 76.8 - - - +
68A GLN* 1.3 58.5 + - - +
70A ALA* 3.1 4.3 + - - +
71A MET* 2.8 47.4 + - + +
82A LEU* 4.0 18.2 - - + -
220A ILE* 3.7 29.6 - - + -
222A THR* 5.1 1.1 - - + -
249A ALA* 4.0 22.0 - - + +
252A THR* 3.9 11.7 - - + -
253A SER* 3.5 39.1 + - - +
256A LEU* 4.6 5.8 - - + -
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Residues in contact with GLN 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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59A ARG 4.8 6.5 + - - +
64A HIS* 2.9 30.4 + - - +
65A PHE* 3.6 30.7 - - - +
67A LEU* 1.3 68.6 - - - +
69A GLN* 1.3 65.7 + - - +
71A MET 3.5 0.2 + - - -
72A CYS* 3.1 31.2 + - - -
80A CYS* 2.9 39.4 - - + +
81A VAL* 4.8 0.9 - - - -
82A LEU* 4.0 23.6 + - + +
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Residues in contact with GLN 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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14A GLY* 3.5 20.0 - - - +
15A ARG 4.4 0.4 - - - +
16A SER* 3.0 24.9 + - - +
18A LYS* 4.3 6.2 + - - -
19A TYR* 3.3 24.6 + - + +
65A PHE 2.9 21.5 + - - +
66A SER 3.8 4.5 - - - +
68A GLN* 1.3 72.0 - - - +
70A ALA* 1.3 58.0 + - - +
72A CYS* 3.4 6.7 + - - +
73A GLU* 3.0 44.6 + - + +
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Residues in contact with ALA 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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13A ALA* 3.5 32.1 - - + +
14A GLY* 3.9 2.6 - - - +
66A SER 3.1 14.3 + - - +
67A LEU* 3.1 10.3 + - - +
69A GLN* 1.3 72.8 - - - +
71A MET* 1.3 60.2 + - - +
73A GLU* 3.3 10.1 + - - +
74A LEU* 2.9 37.4 + - - +
253A SER* 4.9 2.0 - - - +
256A LEU* 3.7 17.0 - - + -
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Residues in contact with MET 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 2.8 42.1 + - + +
70A ALA* 1.3 73.6 - - - +
72A CYS* 1.3 57.8 + - - +
74A LEU* 4.6 5.8 - - + -
75A GLU* 2.9 64.7 + - + +
80A CYS* 3.5 31.2 - - + -
206A GLN* 3.8 3.4 - - - +
212A LEU* 3.6 32.5 - - + -
222A THR* 4.1 15.9 - - + +
224A VAL* 3.8 6.2 - - + +
252A THR* 5.5 0.2 - - - -
256A LEU* 4.4 13.9 - - - -
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Residues in contact with CYS 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 GLN* 3.1 25.2 + - - +
69A GLN* 3.5 6.5 - - - +
71A MET* 1.3 74.5 - - - +
73A GLU* 1.3 59.5 + - - +
76A GLY* 2.8 24.8 + - - -
77A GLY 3.0 25.2 + - - +
78A ALA 3.9 3.6 - - - -
79A GLY* 3.4 46.7 - - - -
80A CYS* 3.7 3.1 - - - -
224A VAL* 4.5 2.2 - - - -
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Residues in contact with GLU 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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9A GLN* 3.7 29.4 + - - +
12A ASN 5.3 0.4 - - - -
13A ALA* 3.8 21.8 + - + +
14A GLY 3.4 16.1 + - - -
69A GLN* 3.0 37.2 + - + +
70A ALA* 3.4 11.4 - - - +
72A CYS* 1.3 78.9 - - - +
74A LEU* 1.3 62.1 + - + +
76A GLY* 3.6 6.5 + - - -
195A LYS* 5.3 1.6 - - - -
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Residues in contact with LEU 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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6A LEU* 4.5 5.9 - - + +
9A GLN* 3.6 36.9 + - + +
10A LEU* 3.8 33.7 - - + -
13A ALA* 4.1 14.1 - - + -
70A ALA 2.9 21.7 + - - +
71A MET* 4.0 8.3 - - + +
73A GLU* 1.3 78.3 - - + +
75A GLU* 1.3 62.5 + - + +
192A VAL* 4.1 19.2 - - + +
195A LYS* 3.3 23.6 - - - +
212A LEU* 6.1 0.7 - - + -
256A LEU* 3.8 31.0 - - + -
259A LEU* 5.9 0.2 - - + -
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Residues in contact with GLU 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 MET* 2.9 37.6 + - + +
74A LEU* 1.3 78.2 - - + +
76A GLY* 1.3 66.4 + - - +
77A GLY 3.5 1.3 - - - -
186A ASN* 4.0 0.7 - - - +
191A GLY* 3.7 24.1 - - - +
192A VAL* 5.3 0.9 - - + -
195A LYS* 4.4 16.1 + - + +
196A ALA* 5.4 1.2 + - - +
197A LEU* 3.7 19.5 + - + +
198A ASP* 5.1 1.0 + - - +
204A SER* 2.6 32.0 + - - +
206A GLN* 2.8 31.7 + - - +
222A THR* 4.7 0.7 + - - -
224A VAL* 3.6 21.5 - - + +
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Residues in contact with GLY 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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72A CYS 2.8 13.3 + - - -
73A GLU 3.6 5.4 + - - -
74A LEU 3.5 3.2 - - - -
75A GLU* 1.3 79.5 - - - +
77A GLY* 1.3 57.7 + - - -
195A LYS* 4.6 9.1 - - - +
197A LEU* 3.6 13.2 - - - +
198A ASP* 5.0 4.8 - - - +
226A ASN* 5.8 0.2 - - - -
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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