Contacts of the helix formed by residues 50 - 64 (chain A) in PDB entry 3O2Q
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 SER 50 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A ILE* 3.6 12.4 - - - +
48A ASN* 2.4 28.9 + - - -
49A ASP* 1.3 73.5 - - - +
51A LYS* 1.3 64.2 + - - +
52A ILE 3.0 0.4 - - - -
53A THR* 3.1 28.8 + - - -
54A VAL* 3.7 5.9 + - - +
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Residues in contact with LYS 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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43A ALA* 4.0 17.1 + - + +
46A ILE* 3.5 39.1 + - + +
47A THR* 4.6 5.2 - - - +
48A ASN 3.1 27.8 + - - +
49A ASP* 3.0 0.6 - - - -
50A SER* 1.3 79.2 + - - +
52A ILE* 1.3 62.2 + - + +
54A VAL* 3.1 6.3 + - - +
55A LEU* 2.9 34.4 + - + +
80A PHE* 4.5 19.4 - - + -
83A ASP* 3.1 28.6 + - - +
85A SER* 5.6 0.4 - - - -
88A VAL* 3.8 27.8 - - + -
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Residues in contact with ILE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ASP* 3.0 20.5 + - + +
51A LYS* 1.3 76.2 - - + +
53A THR* 1.3 61.3 + - - +
55A LEU* 3.1 6.6 + - + +
56A LYS* 2.8 50.5 + - + +
87A GLU* 3.3 46.0 - - + +
88A VAL* 3.8 20.9 - - + +
91A PHE* 3.9 22.9 - - + -
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Residues in contact with THR 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 ASP 4.4 0.4 + - - -
50A SER* 3.1 19.0 + - - -
52A ILE* 1.3 78.9 - - - +
54A VAL* 1.3 64.3 + - + +
56A LYS* 3.4 10.1 + - - +
57A GLN* 3.2 37.4 + - - +
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Residues in contact with VAL 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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39A LEU* 3.2 38.5 - - + +
42A GLN* 3.4 27.6 - - - +
43A ALA* 3.8 12.3 - - + +
46A ILE* 3.8 23.6 - - + -
50A SER 4.3 5.2 - - - +
51A LYS 3.1 9.3 + - - +
53A THR* 1.3 78.1 - - + +
55A LEU* 1.3 63.0 + - - +
57A GLN* 3.1 25.2 + - - +
58A VAL* 3.1 12.4 + - + +
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Residues in contact with LEU 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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40A LEU* 4.2 15.5 - - + -
43A ALA* 3.7 22.7 - - + -
51A LYS* 2.9 29.3 + - + +
52A ILE* 3.1 6.2 + - + +
54A VAL* 1.3 76.9 - - - +
56A LYS* 1.3 57.6 + - - +
58A VAL* 3.3 9.1 + - + +
59A GLN 3.0 21.7 + - - -
77A ILE* 4.9 7.1 - - + +
80A PHE* 3.8 46.0 - - + -
88A VAL* 4.7 6.1 - - + -
91A PHE* 3.4 41.6 - - + -
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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 ILE* 2.8 36.2 + - + +
53A THR* 3.7 8.5 - - - +
54A VAL 3.2 0.2 - - - -
55A LEU* 1.3 75.1 - - - +
57A GLN* 1.3 62.1 + - - +
59A GLN* 3.4 9.5 + - + +
60A GLU* 3.0 22.7 + - - +
91A PHE* 3.7 20.9 - - + -
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Residues in contact with GLN 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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35A ARG* 4.9 4.8 + - - -
39A LEU* 3.5 30.8 - - + +
42A GLN* 4.9 1.6 - - - +
53A THR* 3.2 30.4 + - + +
54A VAL* 3.1 15.1 + - - +
56A LYS* 1.3 71.9 - - - +
58A VAL* 1.3 66.0 - - - +
60A GLU* 3.3 8.4 + - - +
61A LEU* 3.0 29.4 + - + +
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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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36A VAL* 4.1 21.5 - - + +
39A LEU* 3.6 32.5 - - + +
40A LEU* 4.2 19.3 - - + +
54A VAL 3.1 9.9 + - - +
55A LEU* 3.4 12.6 - - + +
56A LYS 3.3 0.2 - - - -
57A GLN* 1.3 76.1 - - - +
59A GLN* 1.3 61.6 + - - +
61A LEU* 3.1 11.5 + - - +
62A ILE* 3.0 29.4 + - + +
77A ILE* 3.3 31.6 - - + -
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Residues in contact with GLN 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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55A LEU 3.0 13.3 + - - +
56A LYS* 3.5 13.8 - - - +
58A VAL* 1.3 74.0 - - - +
60A GLU* 1.3 66.9 + - - +
62A ILE* 4.4 0.4 - - - -
63A ILE* 3.0 42.5 + - + +
64A ASN* 6.2 0.4 - - - +
91A PHE* 3.3 26.0 - - + -
94A GLY 4.6 1.5 - - - +
95A PHE* 3.6 43.4 - - + +
98A GLU* 3.6 22.5 - - - +
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Residues in contact with GLU 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 3.0 10.6 + - - +
57A GLN* 3.3 11.6 + - - +
59A GLN* 1.3 80.3 - - - +
61A LEU* 1.3 64.1 + - + +
64A ASN* 3.0 61.2 + - - +
65A LYS* 3.2 15.6 + - + +
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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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32A THR* 3.9 19.2 - - + +
35A ARG* 3.7 30.3 - - + +
36A VAL* 3.8 21.8 - - + -
39A LEU* 3.7 18.4 - - + -
57A GLN* 3.0 16.2 + - + +
58A VAL 3.1 7.1 + - - +
60A GLU* 1.3 82.4 - - + +
62A ILE* 1.3 58.3 + - - +
65A LYS* 3.3 27.0 + - + +
66A ASP* 2.9 30.7 + - - +
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Residues in contact with ILE 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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36A VAL* 3.7 35.0 - - + -
58A VAL* 3.0 24.2 + - + +
59A GLN 4.1 2.7 - - - +
61A LEU* 1.3 74.7 - - - +
63A ILE* 1.3 68.5 + - + +
66A ASP 3.8 9.3 - - - +
67A PRO* 3.4 16.8 - - - +
69A LEU* 4.3 14.6 - - + -
70A LEU* 3.7 32.6 - - + +
73A PHE* 4.2 22.4 - - + -
77A ILE* 4.4 3.1 - - + -
95A PHE* 4.0 26.5 - - + -
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Residues in contact with ILE 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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59A GLN* 3.0 24.4 + - + +
62A ILE* 1.3 92.1 - - + +
64A ASN* 1.3 69.2 + - - +
67A PRO* 3.6 9.7 - - - +
70A LEU* 4.3 9.6 - - + -
95A PHE* 3.8 22.7 - - + -
98A GLU* 3.7 22.2 - - + +
99A ALA* 3.6 27.8 - - - +
102A ARG* 2.7 53.3 + - + +
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Residues in contact with ASN 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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59A GLN* 6.2 0.4 - - - +
60A GLU* 3.0 43.9 + - - +
63A ILE* 1.3 86.4 - - - +
65A LYS* 1.3 66.7 + - - +
66A ASP 3.5 0.4 - - - -
67A PRO* 4.2 7.6 - - - +
102A ARG* 2.7 33.6 + - - +
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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