Contacts of the strand formed by residues 65 - 72 (chain A) in PDB entry 6Q6Q
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 ARG 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A TYR* 3.8 4.8 - - - -
60A ASN* 3.3 28.2 + - - +
63A THR* 3.2 39.6 + - + +
64A LYS* 1.3 79.1 - - - +
66A ILE* 1.3 76.2 + - - +
67A ARG* 4.1 1.0 + - - +
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Residues in contact with ILE 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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57A SER* 4.7 0.4 - - - -
58A ARG 3.3 16.8 - - - +
59A TYR* 3.6 20.2 - - + -
65A ARG* 1.3 87.2 - - - +
67A ARG* 1.3 60.0 + - - +
68A HIS* 3.7 30.6 + - + +
218A PHE* 3.5 48.2 - - + +
223A MET* 4.3 12.1 - - + -
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Residues in contact with ARG 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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56A ILE 3.7 1.6 - - - +
57A SER* 3.5 3.5 - - - -
58A ARG* 2.9 43.9 + - + +
60A ASN* 6.2 2.7 - - + +
65A ARG 4.1 1.5 + - - +
66A ILE* 1.3 72.5 - - - +
68A HIS* 1.3 69.5 + - - +
69A HIS* 3.7 38.9 + - + +
311A SER* 4.4 4.6 + - - -
314A GLN* 3.7 43.9 + - - +
351A ASN* 4.4 14.1 + - - -
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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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55A MET* 3.9 22.7 - - + -
56A ILE 3.7 2.9 - - - -
57A SER* 2.9 29.1 + - - -
66A ILE* 3.7 35.1 + - + +
67A ARG* 1.3 77.0 - - - +
69A HIS* 1.3 63.5 + - - +
127A THR* 4.5 1.8 - - + -
130A ARG* 3.1 48.6 + - + -
131A ASN* 3.2 37.8 + - - +
216A LEU 5.8 0.2 - - - -
218A PHE* 4.9 5.4 - + + -
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Residues in contact with HIS 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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55A MET* 4.4 0.4 - - - +
56A ILE* 3.0 59.0 + - + +
58A ARG* 5.5 6.3 + - + -
67A ARG* 3.7 35.2 + - - +
68A HIS* 1.3 76.3 - - - +
70A PRO* 1.3 91.2 + - - +
71A ALA* 3.9 15.3 - - + -
127A THR* 3.9 5.7 - - - +
351A ASN* 3.5 40.0 - - + +
352A MET* 4.7 3.4 - - + -
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Residues in contact with PRO 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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53A THR* 4.4 8.5 - - + -
54A VAL 3.3 10.8 - - - +
68A HIS 4.9 0.2 - - - +
69A HIS* 1.3 107.4 + - + +
71A ALA* 1.3 62.0 + - - +
124A SER* 5.3 5.4 - - - +
127A THR* 3.6 27.1 - - + +
131A ASN* 5.3 3.4 - - - +
143A ALA* 6.5 0.4 - - + -
347A SER* 3.8 24.7 - - - +
348A GLN* 4.0 15.4 - - + +
351A ASN* 3.5 24.6 - - - +
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Residues in contact with ALA 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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53A THR* 3.4 3.2 - - - -
54A VAL* 2.9 33.9 + - + +
56A ILE* 4.0 8.1 - - + -
69A HIS* 3.9 11.0 - - + -
70A PRO* 1.3 78.1 - - - +
72A ASN* 1.3 64.5 + - - +
73A ALA 3.6 0.3 + - - -
76A ILE* 3.6 24.9 - - + -
348A GLN* 4.0 9.5 - - - +
352A MET* 3.7 18.2 - - + -
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Residues in contact with ASN 72 (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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47A GLY* 3.4 16.6 + - - +
50A GLY* 3.7 24.5 - - - +
52A CYS* 3.8 14.4 - - - -
53A THR* 3.9 3.8 + - - -
71A ALA* 1.3 70.6 - - - +
73A ALA* 1.3 66.2 + - - +
74A CYS* 3.2 7.3 + - - -
75A LEU* 3.3 11.1 + - + +
76A ILE* 3.4 13.4 - - - +
348A GLN* 3.2 34.4 + - - +
349A ILE* 3.3 25.3 + - + +
352A MET* 3.5 12.3 - - - +
3002A FES 4.0 6.9 - - - -
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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