Contacts of the strand formed by residues 58 - 70 (chain A) in PDB entry 3QNF
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 VAL 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A PRO* 4.0 9.7 + - + +
56A GLU 3.4 1.0 - - - -
57A TYR* 1.3 101.0 - - + +
59A ILE* 1.3 68.9 + - - +
60A PRO 4.3 0.2 - - - -
84A ILE* 4.1 22.2 - - + -
85A THR 3.8 7.4 - - - +
86A ALA* 4.4 6.3 - - + -
90A THR* 3.9 17.5 - - + -
92A THR 4.7 6.5 - - - +
93A ILE* 4.4 12.1 - - + -
94A ILE 5.9 1.1 - - - +
139A LEU* 6.0 1.6 - - + -
194A PHE* 3.9 34.2 - - + -
199A PHE* 3.7 14.4 - - - -
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Residues in contact with ILE 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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56A GLU 3.1 27.4 - - - +
57A TYR 4.7 2.2 - - - +
58A VAL* 1.3 79.4 - - - +
60A PRO* 1.3 80.5 - - + +
61A VAL* 4.8 1.0 - - - +
84A ILE* 3.4 5.0 - - - -
85A THR* 3.1 42.3 + - - +
87A SER* 5.3 8.7 - - - +
199A PHE* 4.1 17.3 - - + -
200A LYS 5.4 2.9 - - - +
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Residues in contact with PRO 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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58A VAL 4.0 0.2 - - - +
59A ILE* 1.3 101.9 - - + +
61A VAL* 1.3 59.7 + - - +
63A TYR* 3.8 20.0 - - + +
82A VAL* 3.8 12.1 - - + -
83A GLU 3.4 6.7 - - - +
84A ILE* 4.0 4.2 - - + -
194A PHE* 3.5 39.3 - - + -
199A PHE* 3.9 31.4 - - + +
200A LYS 3.8 10.0 - - - +
201A ALA* 4.3 2.5 - - + -
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Residues in contact with VAL 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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59A ILE 4.9 1.1 - - - +
60A PRO* 1.3 76.0 - - - +
62A HIS* 1.3 66.2 + - + +
83A GLU* 2.9 39.1 + - + +
84A ILE* 3.9 8.1 - - - +
85A THR* 5.1 8.7 - - + -
144A PRO* 6.6 0.2 - - + -
201A ALA* 3.7 8.6 - - - +
202A SER* 3.3 18.4 + - - -
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Residues in contact with HIS 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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61A VAL* 1.3 86.2 - - + +
63A TYR* 1.3 84.4 + - - +
64A ASP* 4.0 10.0 + - + -
81A LYS 3.9 0.6 - - - +
82A VAL* 3.6 1.7 - - - +
83A GLU* 2.8 55.5 + - + +
201A ALA* 4.2 0.6 - - - +
202A SER* 2.6 28.8 + - - +
204A SER* 3.2 29.3 + - - -
238A VAL* 3.5 16.0 - - + +
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Residues in contact with TYR 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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60A PRO* 3.8 15.2 - - + +
62A HIS* 1.3 85.2 + - - +
64A ASP* 1.3 58.8 + - - +
65A LEU* 3.9 19.3 - - + -
80A THR* 4.4 5.2 - - + -
81A LYS 3.4 4.3 - - - -
82A VAL* 3.9 20.9 - - + -
191A PHE* 4.5 0.9 - + - -
192A PRO 4.2 1.8 - - - -
193A CYS* 3.5 27.5 - - + +
194A PHE* 3.1 36.0 + - - +
199A PHE 5.0 1.0 + - - -
201A ALA* 3.5 24.5 - - + -
202A SER 2.7 8.9 + - - -
203A PHE* 3.2 48.0 - + + -
204A SER 2.9 26.5 + - - +
244A THR* 4.1 5.7 - - + +
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Residues in contact with ASP 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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62A HIS* 4.0 9.3 + - + +
63A TYR* 1.3 71.4 - - - +
65A LEU* 1.3 63.6 + - - +
66A LEU* 5.2 1.4 + - - +
79A THR 3.7 2.1 - - - +
80A THR* 3.5 4.9 - - - -
81A LYS* 2.6 61.9 + - + +
204A SER* 3.5 14.2 - - - -
206A LYS* 3.1 34.9 + - - +
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Residues in contact with LEU 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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63A TYR* 3.9 18.2 - - + -
64A ASP* 1.3 80.6 - - - +
66A LEU* 1.3 55.6 + - - +
67A ILE* 4.1 7.2 - - + -
79A THR 4.0 1.1 - - - -
80A THR* 3.8 22.9 - - + +
191A PHE* 3.5 57.7 - - + -
203A PHE* 4.0 12.3 - - + -
204A SER 2.7 14.5 + - - +
205A ILE* 3.4 23.9 - - + -
206A LYS* 2.6 37.1 + - - +
247A VAL* 4.8 1.1 - - + -
249A PHE* 4.9 4.9 - - + -
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Residues in contact with LEU 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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64A ASP* 5.6 1.6 - - - +
65A LEU* 1.3 73.8 - - - +
67A ILE* 1.3 68.9 + - - +
68A HIS* 4.2 2.2 - - + +
78A GLY* 3.2 7.0 - - - -
79A THR* 3.1 50.0 + - - +
206A LYS* 3.2 31.2 - - + +
208A ARG* 3.5 53.6 - - + +
233A GLU* 3.7 10.1 - - - +
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Residues in contact with ILE 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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65A LEU* 5.0 8.1 - - + -
66A LEU* 1.3 83.5 - - - +
68A HIS* 1.3 63.9 + - - +
69A ALA* 4.0 1.3 + - + -
76A PHE* 4.2 11.7 - - + -
77A TRP 3.8 0.7 - - - -
78A GLY* 4.4 2.7 - - - -
151A TYR* 3.0 30.1 - - + +
162A PHE* 3.6 33.2 - - + -
190A ALA 3.7 12.1 - - - +
191A PHE* 4.7 4.7 - - + -
205A ILE* 5.5 0.2 - - + -
206A LYS 2.8 9.3 + - - -
207A ILE* 3.3 21.6 - - + +
208A ARG* 2.8 24.5 + - - -
249A PHE* 4.0 22.2 - - + -
251A ILE* 5.3 0.4 - - + -
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Residues in contact with HIS 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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66A LEU* 4.2 3.7 - - + +
67A ILE* 1.3 72.1 - - - +
69A ALA* 1.3 63.7 + - - +
70A ASN* 4.8 0.6 - - + +
75A THR 4.3 0.3 - - - +
76A PHE* 3.1 2.6 - - - -
77A TRP* 2.8 49.7 + - + +
208A ARG* 3.6 37.7 + - + +
231A LEU* 3.3 32.7 - - + +
1D NAG 2.7 33.2 + - + -
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Residues in contact with ALA 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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67A ILE* 3.9 2.1 + - + -
68A HIS* 1.3 78.8 - - - +
70A ASN* 1.3 59.9 + - - +
71A LEU* 3.5 15.4 + - + +
75A THR 4.4 0.2 - - - +
76A PHE* 3.5 9.2 - - + -
155A LEU* 4.5 3.1 - - + -
162A PHE* 3.5 33.4 - - + -
208A ARG 3.7 8.2 + - - +
209A ARG* 5.3 0.9 - - - -
251A ILE* 3.6 20.4 - - + +
1D NAG 3.8 12.5 - - - +
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Residues in contact with ASN 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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68A HIS* 4.2 1.7 - - - +
69A ALA* 1.3 70.9 - - - +
71A LEU* 1.3 61.7 + - - +
72A THR* 2.9 11.8 + - - -
73A THR* 2.8 39.6 + - - +
74A LEU* 2.9 24.1 + - - -
75A THR* 2.6 25.0 + - + +
155A LEU* 4.3 1.6 - - - +
210A GLU* 5.0 0.2 - - - -
1D NAG 1.4 70.9 + - - +
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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