Contacts of the helix formed by residues 50 - 67 (chain A) in PDB entry 3QTH
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 PRO 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LEU 3.8 3.4 - - - +
41A ASN* 3.4 34.8 - - + +
42A ALA 3.3 7.2 - - - +
43A ARG* 3.9 28.3 - - + +
48A MSE 3.8 0.4 - - - -
49A PHE* 1.4 92.6 - - + +
51A PHE* 1.3 67.3 + - - +
52A ASN* 3.6 14.4 - - - +
53A VAL* 3.1 17.9 + - + -
54A GLN* 2.9 21.2 + - - +
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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
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25A LEU* 4.9 1.1 - - + -
26A ILE* 4.6 11.0 - - + -
29A VAL* 4.0 30.3 - - + -
39A LEU 3.3 24.0 - - - +
40A LEU* 3.5 20.4 - - + +
42A ALA 2.9 13.6 + - - +
50A PRO* 1.3 68.8 - - - +
52A ASN* 1.3 65.0 + - - +
54A GLN* 3.2 6.3 + - - +
55A ALA* 3.1 20.5 + - + +
84A PHE* 4.8 2.5 - + - -
87A LEU* 4.0 18.8 - - + -
145A VAL* 3.4 49.9 - - + +
148A ILE* 3.7 25.2 - - + +
149A ALA* 4.1 14.8 - - + -
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Residues in contact with ASN 52 (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 LEU* 3.0 35.5 + - + +
41A ASN* 4.3 7.6 + - - +
50A PRO* 3.6 7.8 - - - +
51A PHE* 1.3 81.5 - - - +
53A VAL* 1.4 81.0 + - - +
55A ALA* 3.3 4.2 + - - +
56A LYS* 3.0 26.0 + - - +
81A ILE* 2.9 43.4 + - + +
82A ASP* 3.6 17.6 + - - +
87A LEU* 3.9 13.4 - - + +
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Residues in contact with VAL 53 (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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49A PHE* 3.7 31.2 - - + -
50A PRO* 3.1 25.0 + - + +
52A ASN* 1.4 90.1 + - - +
54A GLN* 1.3 58.9 + - - +
56A LYS* 3.3 13.4 + - + +
57A ILE* 2.9 47.2 + - + +
81A ILE* 4.1 13.0 - - + -
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Residues in contact with GLN 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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48A MSE 4.5 4.2 - - - +
49A PHE* 3.2 25.7 + - - +
50A PRO 2.9 19.5 + - - +
51A PHE* 3.4 8.1 - - - +
53A VAL* 1.3 76.9 - - - +
55A ALA* 1.4 61.1 + - - +
57A ILE* 3.6 0.8 + - - -
58A ALA* 3.1 20.4 + - - +
141A HIS* 2.7 45.5 + - - +
144A MSE 3.4 33.4 - - + +
145A VAL* 3.6 17.0 - - + +
148A ILE* 4.0 6.2 - - + +
178A CL 3.3 24.8 - - - +
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Residues in contact with ALA 55 (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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22A LEU* 4.1 20.6 - - + +
26A ILE* 4.6 3.6 - - + -
51A PHE* 3.1 12.4 + - + +
52A ASN 3.6 8.1 - - - +
54A GLN* 1.4 75.5 - - - +
56A LYS* 1.3 57.8 + - - +
58A ALA* 3.6 2.4 + - - +
59A THR* 2.7 34.9 + - - -
87A LEU* 3.9 25.4 - - + -
90A TYR* 5.7 0.2 - - - -
91A VAL* 5.3 0.7 - - + -
145A VAL* 3.5 17.4 - - + +
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Residues in contact with LYS 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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52A ASN 3.0 13.7 + - - +
53A VAL* 3.3 17.0 + - + +
55A ALA* 1.3 76.3 - - - +
57A ILE* 1.3 58.1 + - + +
59A THR* 3.3 3.3 + - - -
60A ASN* 2.8 36.9 + - - +
76A GLU* 3.4 38.1 + - - -
77A LEU 5.0 1.1 - - - -
81A ILE* 3.9 28.6 - - + +
87A LEU* 4.7 1.3 - - - +
90A TYR* 3.4 35.4 - - + +
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Residues in contact with ILE 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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49A PHE* 3.5 37.0 - - + -
53A VAL* 2.9 31.4 + - + +
54A GLN* 4.0 3.6 - - - +
56A LYS* 1.3 76.3 - - + +
58A ALA* 1.4 54.8 + - - +
60A ASN* 3.2 7.4 + - - +
61A PHE* 2.8 47.6 + - + -
64A ARG* 6.0 0.2 - - - +
141A HIS* 3.5 38.4 - - + +
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Residues in contact with ALA 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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19A LEU* 4.8 0.2 - - - -
22A LEU* 4.7 0.7 - - + -
54A GLN 3.1 17.7 + - - +
55A ALA* 3.7 6.7 - - - +
56A LYS 3.4 0.2 - - - -
57A ILE* 1.4 73.9 - - - +
59A THR* 1.4 62.7 + - - +
61A PHE* 3.2 6.2 + - - +
62A ALA 3.2 8.8 + - - -
138A PHE* 3.2 28.7 - - - +
141A HIS* 3.9 14.5 - - + +
142A ILE* 3.7 37.9 - - + +
145A VAL* 5.5 0.2 - - + -
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Residues in contact with THR 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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19A LEU* 3.9 12.1 - - + +
22A LEU* 3.8 6.4 - - - +
55A ALA 2.7 22.6 + - - -
56A LYS 3.3 5.1 + - - -
58A ALA* 1.4 75.6 - - - +
60A ASN* 1.4 60.8 + - - +
62A ALA* 3.2 6.2 + - - +
63A LEU* 3.2 22.0 + - + +
77A LEU* 4.4 2.5 - - + -
90A TYR* 3.9 27.5 - - + +
91A VAL* 3.8 21.2 - - - +
94A ALA* 3.3 33.2 - - + -
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Residues in contact with ASN 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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56A LYS* 2.8 33.2 + - - +
57A ILE* 3.2 7.4 + - + +
59A THR* 1.4 71.5 - - - +
61A PHE* 1.3 60.6 + - - +
63A LEU* 3.3 10.8 + - - +
64A ARG* 2.8 38.7 + - - +
74A TYR* 2.8 29.9 + - - +
76A GLU* 3.8 10.9 + - - +
77A LEU 3.4 18.9 + - - -
90A TYR* 2.7 28.1 + - - -
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Residues in contact with PHE 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 ILE* 2.8 43.5 + - + -
58A ALA 3.2 8.5 + - - +
60A ASN* 1.3 76.4 - - + +
62A ALA* 1.4 61.0 + - - +
64A ARG* 3.3 39.0 + - - +
65A ALA 3.1 11.8 + - - -
133A PHE* 4.1 15.9 - + - -
134A VAL* 3.0 41.6 - - + +
137A ASN* 3.6 38.6 - - + -
138A PHE* 4.2 10.8 - - - -
141A HIS* 3.8 16.4 - + - -
158B LYS* 4.1 4.9 - - - -
165B HIS* 4.4 9.6 - + - -
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Residues in contact with ALA 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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15A PHE* 4.1 20.4 - - + -
19A LEU* 3.7 27.8 - - + -
58A ALA 3.2 12.0 + - - +
59A THR 3.2 9.4 + - - +
61A PHE* 1.4 75.1 - - - +
63A LEU* 1.3 54.8 - - - +
65A ALA* 3.4 2.8 + - - +
66A CYS* 3.1 34.3 + - - -
98A ILE* 4.0 7.4 - - + -
138A PHE* 4.0 12.9 - - + -
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A THR* 3.2 17.9 + - + +
60A ASN* 3.6 17.7 - - - +
61A PHE 3.3 0.2 - - - -
62A ALA* 1.3 73.5 - - - +
64A ARG* 1.3 59.1 + - - +
66A CYS* 4.5 1.3 - - - +
67A CYS* 2.9 39.1 + - - +
74A TYR* 3.9 16.2 - - + -
75A LYS 5.4 1.3 - - - +
77A LEU* 3.8 38.4 - - + +
94A ALA* 4.1 19.7 - - + -
97A TYR* 3.7 33.4 - - + -
98A ILE* 4.1 12.3 - - + -
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Residues in contact with ARG 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 ILE* 6.0 0.2 - - - +
60A ASN* 2.8 27.1 + - - +
61A PHE* 3.4 40.3 - - + +
63A LEU* 1.3 74.0 - - - +
65A ALA* 1.4 56.4 + - - +
68A PRO* 3.0 22.2 - - - +
74A TYR* 3.6 42.4 - - + +
115A ASP* 2.9 28.8 + - - +
116A THR 3.4 20.0 + - - -
117A ALA* 5.3 0.4 - - - +
129A TYR* 3.3 24.8 + - + +
133A PHE* 3.7 14.7 - - - -
134A VAL* 4.9 2.9 - - + -
165B HIS* 5.6 1.4 + - - -
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Residues in contact with ALA 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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15A PHE* 3.6 30.5 - - + -
61A PHE 3.1 4.9 + - - -
62A ALA 3.6 6.1 - - - +
63A LEU 3.2 0.2 - - - -
64A ARG* 1.4 78.5 - - - +
66A CYS* 1.3 59.6 + - - +
68A PRO* 4.0 2.3 - - - +
69A LEU* 3.2 28.6 - - - +
129A TYR* 4.0 10.5 - - - -
130A MSE 3.9 13.6 - - + +
134A VAL* 3.7 22.4 - - + +
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Residues in contact with CYS 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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8A TYR* 5.0 5.3 + - - +
12A ARG* 4.2 14.8 - - - -
15A PHE* 4.3 17.3 - - - -
62A ALA 3.1 17.5 + - - +
63A LEU 3.3 1.3 + - - +
65A ALA* 1.3 81.4 - - - +
67A CYS* 1.4 65.1 + - - +
68A PRO 3.6 0.2 - - - -
69A LEU* 3.4 14.3 + - - +
70A SER* 3.5 8.5 + - - -
98A ILE* 4.0 30.7 - - + -
101A LEU* 3.7 27.0 - - + +
130A MSE 4.4 6.3 - - - -
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Residues in contact with CYS 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 LEU* 2.9 35.4 + - - +
66A CYS* 1.4 70.8 - - - +
68A PRO* 1.4 63.7 - - + +
70A SER 3.3 6.9 + - - -
72A LYS* 2.8 44.1 + - + +
73A GLU 5.4 0.7 - - - -
74A TYR* 4.1 25.4 - - + -
75A LYS 5.4 1.1 - - - -
97A TYR* 3.5 34.5 - - - -
101A LEU* 4.8 3.8 - - - -
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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