Contacts of the helix formed by residues 49 - 71 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ILE* 3.8 1.4 - - - +
48A GLU* 1.3 77.1 - - - +
50A HIS* 1.3 63.7 + - - -
51A PHE* 3.4 2.2 - - - -
52A ASP* 3.5 5.1 + - - +
53A GLU* 3.1 30.8 + - - +
122A ARG* 4.3 15.0 - - - -
123A THR* 4.3 1.9 - - - +
126A ILE* 3.8 20.7 - - - +
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Residues in contact with HIS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY* 1.3 74.3 - - - -
51A PHE* 1.3 65.1 + - - +
53A GLU* 3.3 11.0 + - - +
54A ALA* 3.1 23.6 + - - +
122A ARG* 5.1 10.7 + - - +
125A ILE* 3.7 25.8 - - + +
126A ILE* 3.8 25.3 - - + +
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Residues in contact with PHE 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A GLY* 6.0 0.4 - - - -
50A HIS* 1.3 78.9 - - - +
52A ASP* 1.3 75.4 - - - +
54A ALA* 3.3 8.0 + - + +
55A ILE* 3.3 49.7 + - + +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.7 21.3 - - + +
46A SER 3.5 13.0 - - - +
47A ILE* 3.7 10.3 - - - -
48A GLU* 2.8 46.1 + - - +
49A GLY* 3.5 5.3 + - - +
50A HIS 3.4 0.4 - - - -
51A PHE* 1.3 92.2 - - - +
53A GLU* 1.3 58.8 + - - +
55A ILE* 3.4 6.7 + - - +
56A ALA* 2.9 28.4 + - - +
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A ILE* 3.5 18.1 - - + +
49A GLY 3.1 19.8 + - - +
50A HIS* 3.5 13.6 + - - +
51A PHE 3.3 0.2 - - - -
52A ASP* 1.3 76.4 - - - +
54A ALA* 1.3 57.6 + - - +
56A ALA* 3.3 4.4 + - - +
57A ALA* 2.9 30.7 + - - +
81A GLY* 3.0 38.4 - - - +
83A PRO* 3.7 17.0 - - + +
126A ILE* 3.6 27.2 - - + +
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Residues in contact with ALA 54 (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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50A HIS 3.1 12.8 + - - +
51A PHE* 3.7 11.2 - - + +
52A ASP 3.3 0.2 - - - -
53A GLU* 1.3 77.4 - - - +
55A ILE* 1.3 64.3 + - + +
57A ALA* 3.6 15.7 + - - +
58A VAL* 3.7 12.5 + - - +
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Residues in contact with ILE 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ALA 5.2 1.3 - - - +
43A GLY* 3.7 33.4 - - - -
44A VAL* 4.2 11.0 - - + +
51A PHE* 3.3 49.2 + - + +
52A ASP* 3.6 9.4 - - - +
53A GLU 3.3 0.4 - - - -
54A ALA* 1.3 76.7 - - + +
56A ALA* 1.3 63.8 + - - +
58A VAL* 3.3 8.4 + - - +
59A GLY* 3.3 16.8 + - - -
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Residues in contact with ALA 56 (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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11A PRO* 3.7 21.3 - - + +
43A GLY* 6.3 0.7 - - - -
44A VAL* 4.7 3.3 - - + +
47A ILE* 3.6 30.3 - - + -
52A ASP 2.9 17.5 + - - +
53A GLU 3.3 5.8 + - - +
55A ILE* 1.3 78.3 - - - +
57A ALA* 1.3 57.1 + - - +
59A GLY* 3.1 3.3 + - - +
60A VAL* 2.8 34.5 + - - +
83A PRO* 4.1 5.8 - - + -
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Residues in contact with ALA 57 (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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53A GLU 2.9 16.6 + - - +
54A ALA* 3.6 10.1 - - - +
55A ILE 3.2 0.4 - - - -
56A ALA* 1.3 75.0 - - - +
58A VAL* 1.3 62.0 + - + +
60A VAL* 3.4 4.9 + - - +
61A LEU* 3.2 29.8 + - + +
83A PRO* 4.1 5.5 - - - +
84A GLY* 3.8 31.4 - - - +
87A ALA* 6.2 0.7 - - + -
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Residues in contact with VAL 58 (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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54A ALA 3.7 10.7 + - - +
55A ILE* 3.3 9.0 + - - +
57A ALA* 1.3 75.5 - - + +
59A GLY* 1.3 60.1 + - - +
61A LEU* 3.2 15.8 + - + +
62A GLU* 3.0 27.1 + - + +
240A GLN* 5.8 0.9 - - - +
241A PHE* 4.2 33.4 - - + -
244A LEU* 4.1 13.1 - - + +
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Residues in contact with GLY 59 (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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40A PRO* 3.7 29.4 - - - +
42A ALA 4.6 6.1 - - - -
55A ILE 3.3 9.5 + - - -
56A ALA* 3.1 7.7 + - - -
58A VAL* 1.3 74.9 - - - +
60A VAL* 1.3 63.0 + - - +
62A GLU* 3.4 8.4 + - - +
63A GLN* 3.3 25.5 + - - +
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Residues in contact with VAL 60 (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 ILE* 4.0 15.8 - - + +
11A PRO* 3.7 31.2 - - + -
56A ALA 2.8 18.3 + - - +
57A ALA 3.4 9.4 - - - +
59A GLY* 1.3 76.1 - - - +
61A LEU* 1.3 52.0 + - + +
63A GLN* 3.1 5.7 + - - +
64A ILE* 2.8 49.8 + - + +
77A ILE* 3.8 32.1 - - + -
83A PRO* 3.8 16.4 - - + +
84A GLY 4.7 1.6 - - - +
88A ALA* 4.3 5.6 - - + -
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Residues in contact with LEU 61 (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 ALA* 3.2 17.1 + - + +
58A VAL* 3.2 19.0 + - + +
60A VAL* 1.3 79.4 - - + +
62A GLU* 1.3 57.1 + - - +
64A ILE* 4.1 3.6 - - + -
65A ARG* 2.9 30.1 + - - +
84A GLY 4.8 1.1 - - - +
87A ALA* 3.6 46.0 - - + +
88A ALA* 3.7 12.3 - - + +
91A LEU* 3.5 20.4 - - + +
244A LEU* 3.9 23.4 - - + +
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Residues in contact with GLU 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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40A PRO* 5.8 2.5 - - + -
41A ARG 6.1 1.1 - - - +
58A VAL* 3.0 13.6 + - + +
59A GLY* 3.5 11.9 - - - +
60A VAL 3.3 0.4 - - - -
61A LEU* 1.3 75.9 - - - +
63A GLN* 1.3 63.7 + - - +
65A ARG* 3.5 21.8 + - - +
66A ALA* 3.3 23.2 + - - +
244A LEU* 3.6 14.7 - - + +
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Residues in contact with GLN 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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7A GLN* 2.7 32.1 + - - +
9A ILE* 3.8 25.1 - - + -
38A VAL* 3.4 32.0 - - + +
39A CYS 3.5 27.2 - - - +
40A PRO* 4.1 5.4 - - + +
41A ARG* 4.5 4.9 + - - +
59A GLY 3.3 11.6 + - - +
60A VAL 3.1 7.7 + - - +
62A GLU* 1.3 80.4 - - - +
64A ILE* 1.3 53.7 + - - +
66A ALA* 3.2 10.6 + - - +
67A GLY 2.8 19.1 + - - -
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Residues in contact with ILE 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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7A GLN* 4.0 3.1 - - - -
9A ILE* 3.7 12.1 - - + -
60A VAL* 2.8 27.7 + - + +
61A LEU* 3.6 10.5 - - - +
63A GLN* 1.3 72.1 - - - +
65A ARG* 1.3 58.1 + - - +
67A GLY* 3.2 1.4 + - - -
68A ARG* 2.9 30.1 + - + +
75A HIS* 3.6 34.5 - - + +
77A ILE* 5.4 0.2 - - + -
88A ALA* 3.8 29.8 - - + +
91A LEU* 3.8 19.1 - - + -
92A ALA* 3.7 29.8 - - + +
96A VAL* 4.2 5.6 - - + -
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Residues in contact with ARG 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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61A LEU 2.9 17.3 + - - +
62A GLU* 3.5 24.2 + - - +
64A ILE* 1.3 77.9 - - - +
66A ALA* 1.3 75.2 + - - +
69A GLU* 3.0 60.3 + - - +
91A LEU* 4.0 3.1 - - + +
243A SER* 3.1 31.0 + - - +
244A LEU* 3.3 25.5 - - - +
246A PRO* 3.6 17.7 - - + -
247A PHE* 3.4 14.8 - - + -
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Residues in contact with ALA 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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7A GLN* 4.5 1.3 - - - +
62A GLU 3.3 11.2 + - - +
63A GLN* 3.2 22.5 + - - +
65A ARG* 1.3 97.3 - - - +
67A GLY* 1.3 64.1 + - - +
69A GLU* 3.3 8.5 + - - +
70A GLN* 3.1 35.7 + - - +
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Residues in contact with GLY 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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7A GLN* 3.5 23.3 - - - +
63A GLN 2.8 13.7 + - - -
64A ILE 3.6 2.9 - - - -
66A ALA* 1.3 74.7 - - - +
68A ARG* 1.3 55.7 + - - +
70A GLN* 3.2 11.6 + - - +
71A GLY 3.0 21.8 + - - -
72A VAL* 3.1 24.6 + - - +
75A HIS* 4.0 0.2 - - - -
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Residues in contact with ARG 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 ILE* 2.9 17.9 + - + +
67A GLY* 1.3 71.4 - - - +
69A GLU* 1.3 63.9 + - - +
71A GLY* 3.2 14.0 + - - +
72A VAL* 5.0 2.5 - - - +
75A HIS* 4.1 6.1 - - + +
91A LEU* 2.8 38.7 + - - +
92A ALA* 5.1 4.5 - - - -
93A GLN* 4.3 21.9 + - + +
231A PHE* 3.4 37.6 - - - -
232A PRO* 5.7 0.4 - - - +
245A ASN* 4.5 1.8 + - - -
247A PHE* 3.4 61.6 + - + +
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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 ARG* 3.0 52.9 + - - +
66A ALA* 3.5 9.5 - - - +
68A ARG* 1.3 76.4 - - - +
70A GLN* 1.3 61.3 + - + +
71A GLY* 3.5 0.7 + - - -
246A PRO* 3.8 12.8 - - - +
247A PHE* 3.8 17.9 - - + -
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Residues in contact with GLN 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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5A ARG* 2.6 35.5 + - - +
7A GLN* 4.6 6.7 - - - +
36A LEU* 3.9 23.8 - - - +
66A ALA* 3.1 25.6 + - - +
67A GLY* 3.2 16.3 + - - +
69A GLU* 1.3 77.1 - - + +
71A GLY* 1.3 53.8 + - - +
72A VAL* 3.5 6.3 - - + +
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Residues in contact with GLY 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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5A ARG* 3.4 11.5 + - - -
67A GLY 3.0 3.8 + - - -
68A ARG* 3.2 14.5 + - - -
69A GLU 3.2 1.2 - - - -
70A GLN* 1.3 78.9 - - - +
72A VAL* 1.3 66.8 + - - +
73A ASP* 3.9 5.2 + - - +
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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