Contacts of the strand formed by residues 69 - 75 (chain A) in PDB entry 1QQG
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 CYS 69 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A ILE* 4.2 3.4 - - - -
65A PRO 4.1 8.3 - - - -
66A LEU* 2.9 20.8 + - - +
67A GLU 4.7 1.8 - - - +
68A SER* 1.3 77.0 - - - +
70A PHE* 1.3 57.8 + - - +
71A ASN 4.4 7.9 - - - +
72A ILE* 4.4 8.7 - - + -
86A LEU* 3.7 35.9 - - - -
87A TYR 3.2 9.4 - - - +
88A THR* 3.9 16.6 - - - +
114A HIS* 2.7 39.7 + - + +
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Residues in contact with PHE 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 SER 3.7 3.1 + - - +
69A CYS* 1.3 73.2 - - - +
71A ASN* 1.3 72.6 + - + +
87A TYR* 2.9 29.5 + - + -
88A THR 3.7 23.6 - - - -
89A ARG* 4.4 4.9 - - - -
114A HIS* 4.6 4.8 + - - -
159A ALA* 4.4 16.1 - - + +
160A PHE* 3.7 34.3 - + - -
163A VAL* 3.8 15.9 - - + -
184A ARG* 4.3 15.9 - - + -
186A CYS* 4.5 5.8 - - - -
195A VAL* 5.9 5.4 - - + -
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Residues in contact with ASN 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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69A CYS* 3.3 1.9 - - - +
70A PHE* 1.3 100.5 + - + +
72A ILE* 1.3 74.5 + - - +
73A ASN* 2.5 35.5 + - - +
87A TYR* 2.9 34.3 + - + +
114A HIS* 4.8 2.2 + - - -
159A ALA* 5.9 0.2 - - - +
160A PHE* 3.2 30.0 + - + +
163A VAL* 3.2 24.6 - - + +
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Residues in contact with ILE 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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66A LEU* 5.3 3.1 - - + -
69A CYS* 4.4 15.7 - - + -
71A ASN* 1.3 85.2 + - - +
73A ASN* 1.3 74.6 + - - +
84A VAL* 4.4 12.6 - - + -
85A ALA 3.3 10.8 - - - +
86A LEU* 4.7 7.9 - - + -
107A TYR* 3.7 30.3 + - + -
110A LEU* 4.1 36.8 - - + +
111A LEU* 4.4 13.4 - - + +
114A HIS* 3.8 33.2 - - + -
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Residues in contact with ASN 73 (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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71A ASN* 2.5 30.4 + - - +
72A ILE* 1.3 77.1 - - - +
74A LYS* 1.3 63.6 + - - +
75A ARG* 3.2 27.4 + - + +
84A VAL* 3.5 2.1 - - - +
85A ALA* 2.7 42.3 + - - +
87A TYR* 4.1 6.7 - - + -
107A TYR* 4.2 9.4 + - - -
161A LYS 3.4 18.3 - - - +
162A GLU* 3.7 4.4 - - - +
163A VAL 2.9 30.3 + - - +
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Residues in contact with LYS 74 (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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73A ASN* 1.3 74.4 + - - +
75A ARG* 1.3 75.0 + - - +
83A LEU 3.4 5.8 - - - -
84A VAL* 4.6 0.7 - - + +
100A GLU* 5.4 3.8 + - - +
103A GLN* 3.4 26.0 + - + +
104A ASP* 2.8 36.5 + - - +
107A TYR* 3.3 51.0 - - + -
108A GLN* 4.7 0.8 - - - +
162A GLU* 5.1 0.2 - - - +
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Residues in contact with ARG 75 (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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73A ASN* 3.2 14.6 + - + +
74A LYS* 1.3 88.6 + - - +
76A ALA* 1.3 67.5 + - - +
81A LYS 3.9 0.2 - - - +
83A LEU* 2.9 43.7 + - + -
85A ALA* 4.2 14.6 - - + -
87A TYR* 3.6 15.8 + - - +
92A HIS* 5.7 0.9 - - - +
103A GLN* 3.3 7.7 + - - -
162A GLU* 2.7 27.1 + - - -
163A VAL 2.7 48.7 + - - +
164A TRP* 3.5 33.0 - - - +
245A VAL* 6.1 2.2 - - - -
248A ASN* 4.7 8.5 - - - +
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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