Contacts of the helix formed by residues 61 - 76 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLN* 3.0 41.2 + - + +
31B ALA* 4.2 29.2 - - + +
34B LEU* 4.8 4.7 - - + -
54B LEU* 3.7 11.4 - - - -
57B GLY* 4.6 5.4 - - - +
60B GLY* 1.3 77.7 - - - +
62B LEU* 1.3 68.1 + - - +
63B THR* 3.1 11.7 + - - -
64B HIS* 2.8 23.2 + - + +
65B PHE* 3.0 26.5 + - - -
246B ALA* 5.2 0.4 - - + -
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 4.9 8.1 - - + +
27A VAL* 5.6 0.2 - - + -
18B LYS* 3.9 17.0 - - + +
19B TYR* 3.5 36.8 - - + -
21B LEU* 4.3 10.3 - - + -
26B SER* 5.6 0.4 - - - -
27B VAL* 4.3 24.7 - - + -
29B GLN* 3.2 27.1 + - + +
52B GLY 5.9 0.2 - - - +
54B LEU* 3.7 16.9 - - + +
61B THR* 1.3 76.0 - - - +
63B THR* 1.3 56.1 + - - +
65B PHE* 3.3 12.3 + - + -
66B SER* 3.0 26.0 + - - -
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Residues in contact with THR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 4.2 7.7 + - - +
27B VAL* 2.6 27.7 + - - +
28B ILE* 4.4 2.0 - - - -
29B GLN* 2.8 22.2 + - - +
61B THR* 3.1 7.3 + - - -
62B LEU* 1.3 74.8 - - - +
64B HIS* 1.3 64.0 + - - +
66B SER* 3.5 4.7 + - - -
67B LEU* 3.3 19.9 + - - +
246B ALA* 3.3 32.5 - - + +
249B ALA* 4.1 2.8 - - + +
250B TYR* 3.8 22.4 - - + +
253B SER* 4.9 0.9 + - - -
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Residues in contact with HIS 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLY 4.7 4.0 + - - -
59B ARG 5.1 0.4 - - - +
60B GLY* 3.4 15.4 - - - -
61B THR* 2.8 44.9 + - - +
63B THR* 1.3 75.2 - - - +
65B PHE* 1.3 66.3 + - - +
67B LEU* 3.1 4.2 + - - +
68B GLN* 2.9 36.9 + - - +
82B LEU* 4.0 21.1 - - + +
243B MET* 5.0 5.6 - - + +
244B VAL* 2.7 31.6 + - - +
245B ASP 3.7 2.5 - - - -
246B ALA* 3.5 29.7 + - - +
249B ALA* 4.0 10.1 - - - +
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Residues in contact with PHE 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.4 29.6 + + + +
49B ARG 5.9 2.0 - - - -
52B GLY* 3.2 40.6 - - - -
53B GLU 3.9 15.9 - - - -
54B LEU* 3.8 23.3 - - + -
59B ARG* 4.0 14.8 - - + -
60B GLY 3.4 27.4 - - - -
61B THR 3.0 22.1 + - - +
62B LEU* 3.3 9.6 + - + -
64B HIS* 1.3 76.2 - - + +
66B SER* 1.3 56.8 + - - +
68B GLN* 3.5 19.2 + - - +
69B GLN* 2.9 29.8 + - - +
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Residues in contact with SER 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY* 2.6 30.8 + - - -
15B ARG* 4.9 0.5 - - - +
19B TYR* 3.7 24.7 - - - +
26B SER* 3.6 22.3 - - - -
62B LEU 3.0 16.0 + - - -
63B THR 3.7 6.3 - - - -
64B HIS 3.1 0.2 - - - -
65B PHE* 1.3 73.4 - - - +
67B LEU* 1.3 65.6 + - - +
69B GLN* 3.3 1.4 + - - +
70B ALA* 3.0 22.0 + - - +
253B SER* 4.3 4.7 + - - -
257B ARG* 5.3 3.1 + - - -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B THR 3.3 9.5 + - - +
64B HIS 3.1 7.7 + - - +
66B SER* 1.3 78.1 - - - +
68B GLN* 1.3 59.3 + - - +
70B ALA* 3.1 3.9 + - - +
71B MET* 2.8 50.0 + - + +
82B LEU* 3.9 15.7 - - + -
220B ILE* 3.7 29.6 - - + -
222B THR* 5.2 0.7 - - + -
249B ALA* 3.9 23.1 - - + +
252B THR* 3.8 13.5 - - + -
253B SER* 3.4 36.8 + - - +
256B LEU* 4.5 5.4 - - + -
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Residues in contact with GLN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B ARG 5.0 5.9 + - - +
64B HIS* 2.9 25.6 + - - +
65B PHE* 3.6 29.5 - - - +
67B LEU* 1.3 78.3 - - - +
69B GLN* 1.3 62.7 + - - +
71B MET 3.4 0.3 + - - -
72B CYS* 3.0 30.2 + - - -
80B CYS* 2.9 42.3 - - + +
81B VAL* 4.8 1.0 - - - -
82B LEU* 4.0 24.3 + - + +
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Residues in contact with GLN 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLY* 3.7 16.9 - - - +
15B ARG 4.6 0.2 - - - +
16B SER* 3.0 25.5 + - - +
18B LYS* 5.3 3.1 - - - -
19B TYR* 3.5 19.9 + - - +
65B PHE 2.9 17.6 + - - +
66B SER 3.6 4.9 - - - +
68B GLN* 1.3 74.6 - - - +
70B ALA* 1.3 62.3 + - - +
72B CYS* 3.4 7.3 + - - +
73B GLU* 3.0 44.9 + - + +
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Residues in contact with ALA 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA* 3.4 30.1 - - + +
14B GLY* 3.9 8.0 - - - +
66B SER 3.0 13.3 + - - +
67B LEU* 3.1 10.3 + - - +
69B GLN* 1.3 76.6 - - - +
71B MET* 1.3 57.3 + - - +
73B GLU* 3.4 2.8 + - - +
74B LEU* 2.9 37.1 + - - +
253B SER* 5.0 2.2 - - - +
256B LEU* 3.7 22.0 - - + -
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Residues in contact with MET 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B LEU* 2.8 42.6 + - + +
68B GLN 3.8 0.9 - - - +
70B ALA* 1.3 70.6 - - - +
72B CYS* 1.3 58.3 - - - +
74B LEU* 3.3 5.7 + - + -
75B GLU* 2.9 65.2 + - + +
80B CYS* 3.5 31.2 - - - -
206B GLN* 3.9 3.4 - - - +
212B LEU* 3.5 33.9 - - + -
222B THR* 4.0 15.9 - - + +
224B VAL* 3.8 6.8 - - + +
256B LEU* 4.3 13.5 - - - -
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Residues in contact with CYS 72 (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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68B GLN* 3.0 22.2 + - - +
69B GLN* 3.7 6.5 - - - +
71B MET* 1.3 75.3 - - - +
73B GLU* 1.3 55.3 + - - +
76B GLY* 2.8 28.9 + - - -
77B GLY 2.9 23.3 + - - +
78B ALA 3.9 3.8 - - - -
79B GLY* 3.3 47.3 - - - -
80B CYS* 3.6 2.7 - - - -
224B VAL* 4.4 2.7 - - - -
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Residues in contact with GLU 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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9B GLN* 3.7 28.9 + - - +
12B ASN 5.0 1.0 - - - +
13B ALA* 3.9 21.3 + - + +
14B GLY 3.5 18.2 + - - -
69B GLN* 3.0 34.2 + - + +
70B ALA 3.5 6.7 - - - +
72B CYS* 1.3 78.0 - - - +
74B LEU* 1.3 64.9 + - - +
76B GLY* 3.5 6.5 + - - -
195B LYS* 5.1 1.6 + - - -
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Residues in contact with LEU 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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6B LEU* 4.3 7.2 - - + +
9B GLN* 3.5 35.5 - - + +
10B LEU* 3.7 34.8 - - + +
13B ALA* 4.2 13.9 - - + -
70B ALA 2.9 25.4 + - - +
71B MET* 4.1 8.1 - - + +
73B GLU* 1.3 73.9 - - - +
75B GLU* 1.3 62.4 + - + +
191B GLY 4.5 1.6 - - - +
192B VAL* 4.3 16.9 - - + +
195B LYS* 3.3 25.1 - - - +
212B LEU* 6.0 0.2 - - + -
256B LEU* 3.9 30.7 - - + -
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B MET* 2.9 33.2 + - + +
74B LEU* 1.3 79.8 - - + +
76B GLY* 1.3 63.8 + - - +
186B ASN* 4.2 0.5 - - - +
191B GLY* 3.6 24.9 - - - +
192B VAL* 5.4 0.9 - - + -
195B LYS* 3.6 14.5 + - - +
196B ALA* 5.3 1.0 + - - +
197B LEU* 3.6 20.6 + - + +
198B ASP* 5.4 0.5 - - - +
204B SER* 2.6 35.5 + - - +
206B GLN* 2.9 29.7 + - - +
222B THR* 4.7 1.2 + - - -
224B VAL* 3.7 24.4 - - + +
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B CYS 2.8 13.6 + - - -
73B GLU 3.5 5.2 + - - -
74B LEU 3.5 3.0 + - - -
75B GLU* 1.3 79.4 - - - +
77B GLY* 1.3 58.4 + - - -
195B LYS* 3.9 8.7 - - - +
197B LEU* 3.8 10.8 - - - +
198B ASP* 5.7 2.1 - - - +
226B ASN* 5.9 0.7 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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