Contacts of the helix formed by residues 49 - 71 (chain B) in PDB entry 3QVL
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 49 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47B ILE* 3.8 1.8 - - - +
48B GLU* 1.3 76.1 - - - +
50B HIS* 1.3 63.4 + - - -
51B PHE 3.4 2.5 - - - -
52B ASP* 3.4 4.2 + - - +
53B GLU* 3.1 30.3 + - - +
122B ARG* 4.3 15.3 - - - -
123B THR* 4.2 6.1 - - - +
126B ILE* 3.8 17.6 - - - +
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Residues in contact with HIS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY* 1.3 72.1 - - - -
51B PHE* 1.3 65.5 + - - +
53B GLU* 3.3 11.1 + - - +
54B ALA* 3.1 22.3 + - - +
122B ARG* 5.1 10.9 + - - +
125B ILE* 3.7 26.4 - - + +
126B ILE* 3.7 26.0 - - + +
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 6.2 0.7 - - + -
49B GLY 3.4 0.2 - - - -
50B HIS* 1.3 77.4 - - - +
52B ASP* 1.3 77.8 + - - +
54B ALA* 3.2 17.6 + - + +
55B ILE* 3.3 42.6 + - + +
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Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B VAL* 3.7 21.5 - - + +
46B SER 3.4 12.4 - - - +
47B ILE* 3.8 9.4 - - - -
48B GLU* 2.9 46.2 + - - +
49B GLY 3.4 6.4 + - - +
50B HIS 3.3 0.4 - - - -
51B PHE* 1.3 93.2 - - - +
53B GLU* 1.3 57.7 + - - +
55B ILE* 3.4 5.5 + - - +
56B ALA* 2.9 28.6 + - - +
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Residues in contact with GLU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ILE* 3.5 19.5 - - + +
49B GLY 3.1 21.0 + - - +
50B HIS* 3.5 11.0 + - - +
51B PHE 3.2 0.4 - - - -
52B ASP* 1.3 74.6 - - - +
54B ALA* 1.3 54.6 + - - +
56B ALA* 3.3 4.8 + - - +
57B ALA* 2.8 35.7 + - - +
79B SER* 5.3 0.2 + - - -
80B PHE 4.1 3.5 - - - +
81B GLY* 3.3 35.4 - - - +
83B PRO* 3.7 15.8 - - + +
126B ILE* 3.4 30.8 - - + +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B HIS 3.1 12.7 + - - +
51B PHE* 3.2 12.5 + - + +
53B GLU* 1.3 76.9 - - - +
55B ILE* 1.3 62.1 + - + +
57B ALA* 3.6 13.3 + - - +
58B VAL* 3.6 15.9 + - - +
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Residues in contact with ILE 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B ALA 5.3 0.6 - - - +
43B GLY* 3.8 33.1 - - - -
44B VAL* 4.2 10.1 - - + +
51B PHE* 3.3 45.1 + - + +
52B ASP* 3.8 9.6 - - - +
53B GLU 3.3 0.2 - - - -
54B ALA* 1.3 75.1 - - + +
56B ALA* 1.3 66.3 + - - +
58B VAL* 3.3 8.1 + - - +
59B GLY* 3.1 17.8 + - - -
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Residues in contact with ALA 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PRO* 3.9 20.2 - - + +
44B VAL* 4.7 2.4 - - + +
47B ILE* 3.7 29.8 - - + -
52B ASP 2.9 17.9 + - - +
53B GLU* 3.6 5.6 - - - +
55B ILE* 1.3 77.5 - - - +
57B ALA* 1.3 52.7 + - - +
59B GLY* 3.2 2.5 + - - +
60B VAL* 2.7 38.8 + - - +
83B PRO* 4.0 7.2 - - + -
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Residues in contact with ALA 57 (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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53B GLU 2.8 17.2 + - - +
54B ALA* 3.6 10.8 - - - +
55B ILE 3.2 0.4 - - - -
56B ALA* 1.3 77.2 - - - +
58B VAL* 1.3 58.6 + - + +
60B VAL* 3.3 4.7 + - - +
61B LEU* 3.0 32.7 + - + +
83B PRO* 4.0 4.2 - - - +
84B GLY* 3.8 31.7 - - - +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ALA 3.6 9.8 + - - +
55B ILE* 3.3 9.6 + - - +
57B ALA* 1.3 76.2 - - + +
59B GLY* 1.3 60.8 + - - +
61B LEU* 3.3 16.8 + - + +
62B GLU* 2.9 27.7 + - + +
241B PHE* 4.8 18.6 - - + -
244B LEU* 3.9 22.3 - - + +
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Residues in contact with GLY 59 (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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40B PRO* 3.7 35.8 - - - +
42B ALA 4.7 5.2 - - - -
55B ILE 3.1 12.8 + - - -
56B ALA* 3.2 4.9 + - - -
58B VAL* 1.3 74.9 - - - +
60B VAL* 1.3 64.6 + - - +
62B GLU* 3.4 8.2 + - - +
63B GLN* 3.2 20.1 + - - +
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Residues in contact with VAL 60 (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 ILE* 4.0 14.3 - - + +
11B PRO* 3.8 30.3 - - + -
40B PRO* 4.5 0.2 - - - +
56B ALA 2.7 20.5 + - - +
57B ALA 3.4 9.0 - - - +
58B VAL 3.3 0.2 - - - -
59B GLY* 1.3 72.5 - - - +
61B LEU* 1.3 51.7 + - + +
63B GLN* 3.1 4.3 + - - +
64B ILE* 2.7 52.3 + - + +
77B ILE* 3.8 31.2 - - + -
83B PRO* 3.7 17.7 - - + +
84B GLY 4.7 1.1 - - - +
88B ALA* 4.1 6.1 - - + -
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Residues in contact with LEU 61 (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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57B ALA* 3.0 20.1 + - + +
58B VAL* 3.3 19.3 + - + +
60B VAL* 1.3 75.3 - - - +
62B GLU* 1.3 56.7 + - - +
64B ILE* 4.1 2.2 - - - -
65B ARG* 2.9 30.5 + - - +
84B GLY 4.8 1.3 - - - +
87B ALA* 3.7 45.5 - - + +
88B ALA* 3.7 12.8 - - + +
91B LEU* 3.5 22.2 - - + +
244B LEU* 4.0 24.8 - - + +
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Residues in contact with GLU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PRO* 5.6 3.6 - - + -
41B ARG 6.0 1.6 - - - +
58B VAL* 2.9 14.9 + - + +
59B GLY* 3.5 12.8 - - - +
60B VAL 3.3 0.2 - - - -
61B LEU* 1.3 76.5 - - - +
63B GLN* 1.3 64.3 + - + +
65B ARG* 3.5 26.9 + - - +
66B ALA* 3.1 21.1 + - - +
244B LEU* 3.6 15.2 - - + +
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Residues in contact with GLN 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B GLN* 2.7 32.2 + - - +
9B ILE* 3.8 24.2 - - + -
38B VAL* 3.4 30.0 - - + +
39B CYS 3.4 32.7 - - - +
40B PRO* 4.1 6.2 - - + +
41B ARG* 4.4 5.2 + - - +
59B GLY 3.2 10.0 + - - +
60B VAL 3.1 7.6 + - - +
62B GLU* 1.3 79.1 - - - +
64B ILE* 1.3 55.9 + - - +
65B ARG 3.2 0.2 - - - -
66B ALA* 3.5 12.4 - - - +
67B GLY 2.8 18.9 + - - -
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Residues in contact with ILE 64 (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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7B GLN* 4.0 2.9 - - - -
9B ILE* 3.7 9.2 - - + -
60B VAL* 2.7 30.5 + - + +
61B LEU* 3.6 8.1 - - - +
63B GLN* 1.3 70.5 - - - +
65B ARG* 1.3 58.3 + - - +
67B GLY* 3.3 0.7 + - - -
68B ARG* 2.8 30.5 + - + +
75B HIS* 3.5 36.5 - - + +
77B ILE* 5.3 0.2 - - + -
88B ALA* 3.7 29.6 - - + +
91B LEU* 3.8 18.6 - - + -
92B ALA* 3.7 29.2 - - + +
96B VAL* 4.1 7.9 - - + -
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Residues in contact with ARG 65 (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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155A ASP* 3.2 34.2 + - - +
157A SER* 5.9 2.6 - - - -
61B LEU 2.9 18.5 + - - +
62B GLU* 3.5 26.4 + - - +
64B ILE* 1.3 76.4 - - - +
66B ALA* 1.3 72.8 + - - +
69B GLU* 2.8 59.8 + - - +
91B LEU* 4.4 2.2 - - - -
243B SER* 3.0 28.9 + - - +
244B LEU* 3.5 13.4 - - - +
246B PRO* 3.5 22.0 - - + -
247B PHE* 3.5 12.8 - - + -
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Residues in contact with ALA 66 (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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7B GLN* 4.4 0.9 - - - +
62B GLU 3.1 11.9 + - - +
63B GLN* 3.2 26.6 + - - +
65B ARG* 1.3 95.2 - - - +
67B GLY* 1.3 61.9 + - - +
69B GLU* 3.3 7.8 - - - +
70B GLN* 3.1 39.9 + - - +
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Residues in contact with GLY 67 (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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7B GLN* 3.4 23.5 - - - +
63B GLN 2.8 15.2 + - - -
64B ILE 3.7 1.6 - - - -
66B ALA* 1.3 71.3 - - - +
68B ARG* 1.3 59.5 + - - +
70B GLN* 3.1 10.5 + - - +
71B GLY 3.0 21.8 + - - -
72B VAL* 3.1 26.4 + - - +
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Residues in contact with ARG 68 (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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45A PRO* 4.5 13.3 - - - +
64B ILE 2.8 20.0 + - - +
67B GLY* 1.3 70.7 - - - +
69B GLU* 1.3 62.1 + - - +
71B GLY* 3.2 14.4 + - - +
72B VAL* 4.9 2.5 - - - +
75B HIS* 4.0 9.0 - - + +
91B LEU* 2.8 39.0 + - - +
92B ALA* 5.1 2.2 - - - -
93B GLN* 4.3 23.2 + - + +
231B PHE* 3.5 36.4 - - - -
232B PRO* 5.6 0.4 - - - +
245B ASN* 4.5 1.4 + - - -
247B PHE* 3.3 63.2 - - + +
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Residues in contact with GLU 69 (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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149A PRO* 3.5 30.9 - - + +
151A LEU* 2.9 43.6 - - + +
152A ALA* 4.1 6.9 - - + +
155A ASP* 3.3 33.9 - - - +
65B ARG* 2.8 33.9 + - - +
66B ALA* 3.3 8.8 - - - +
67B GLY 3.2 0.2 - - - -
68B ARG* 1.3 77.1 - - - +
70B GLN* 1.3 61.1 + - + +
71B GLY 3.7 0.2 + - - -
246B PRO* 3.9 5.2 - - - +
247B PHE* 3.9 9.6 - - + -
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Residues in contact with GLN 70 (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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149A PRO* 5.1 6.5 - - + -
5B ARG* 2.8 31.1 + - - +
7B GLN* 4.9 4.7 + - - +
36B LEU* 3.9 25.9 - - - +
66B ALA* 3.1 27.7 + - - +
67B GLY* 3.1 9.6 + - - +
69B GLU* 1.3 77.0 - - + +
71B GLY* 1.3 58.8 + - - +
72B VAL* 4.0 7.3 - - + +
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Residues in contact with GLY 71 (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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5B ARG* 2.9 14.6 + - - -
67B GLY 3.0 3.0 + - - -
68B ARG* 3.2 14.2 + - - -
69B GLU 3.4 0.6 + - - -
70B GLN* 1.3 79.4 - - - +
72B VAL* 1.3 66.1 + - - +
73B ASP* 4.0 5.4 + - - +
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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
------------------------------------------------------------
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