Contacts of the strand formed by residues 79 - 86 (chain Z) in PDB entry 2Q4G
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 MET 79 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47Z VAL* 4.0 8.5 - - + -
49Z GLU* 3.3 35.0 - - + -
53Z ASP* 3.7 23.6 - - + +
54Z VAL* 4.4 2.5 - - - +
57Z VAL* 3.7 30.5 - - + -
60Z GLN* 5.5 0.9 - - - +
75Z SER* 4.2 8.7 - - - -
77Z SER* 4.6 11.2 - - - +
78Z SER* 1.3 77.5 - - - +
80Z HIS* 1.3 67.1 + - - +
81Z ILE* 3.4 6.8 + - + +
103Z GLU* 3.2 7.8 - - - -
104Z ARG 2.6 36.3 + - - +
106Z ILE* 3.7 23.6 - - + -
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Residues in contact with HIS 80 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Z PRO* 4.0 28.6 - - + +
47Z VAL* 3.5 2.3 - - - +
48Z HIS* 2.5 55.8 + - + +
49Z GLU* 3.0 27.2 + - - +
79Z MET* 1.3 69.7 - - - +
81Z ILE* 1.3 58.7 + - - +
102Z LYS 3.6 4.2 + - - +
103Z GLU* 2.9 39.0 + - - +
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Residues in contact with ILE 81 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Z PRO 5.0 0.9 - - - +
45Z THR* 4.2 12.8 - - + -
46Z PHE 3.2 13.7 - - - +
47Z VAL* 4.0 12.1 - - + -
48Z HIS* 3.9 3.0 + - - -
79Z MET 3.8 9.4 - - - +
80Z HIS* 1.3 80.4 - - - +
82Z THR* 1.3 60.2 + - - +
83Z ASP* 4.1 15.3 - - - +
101Z PRO* 3.2 3.8 - - - +
102Z LYS* 2.7 66.8 + - + +
104Z ARG* 4.1 8.1 - - + +
106Z ILE* 3.8 24.7 - - + -
123Z SER* 4.0 26.2 - - - -
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Residues in contact with THR 82 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Z SER* 3.2 14.6 + - - +
25Z TYR* 3.7 18.8 - - + -
26Z CYS* 4.0 3.6 - - - -
45Z THR* 3.6 1.4 - - - -
46Z PHE* 2.9 36.7 + - - +
48Z HIS* 2.8 30.6 + - - -
81Z ILE* 1.3 70.6 + - - +
83Z ASP* 1.3 68.4 + - - +
84Z CYS 4.0 0.3 + - - -
99Z THR* 3.5 31.9 - - + -
100Z SER 3.5 3.4 - - - -
101Z PRO* 3.3 11.8 - - - +
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Residues in contact with ASP 83 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Z CYS* 3.6 1.6 - - - -
43Z VAL* 5.8 4.3 - - + -
44Z ASN 3.7 3.6 - - - +
45Z THR* 2.4 40.0 + - - +
81Z ILE* 4.1 5.1 - - - +
82Z THR* 1.3 73.7 - - - +
84Z CYS* 1.3 62.0 + - - +
85Z ARG* 5.7 5.2 - - + +
98Z ARG* 3.3 8.3 - - - +
99Z THR* 3.4 2.6 - - - -
100Z SER* 2.7 49.6 + - - +
102Z LYS* 2.5 34.3 + - - +
123Z SER* 4.4 5.5 + - - -
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Residues in contact with CYS 84 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Z TYR* 4.6 0.2 - - - -
26Z CYS* 2.0 50.5 - - + -
30Z MET* 4.0 13.2 - - + -
42Z PRO 3.8 0.5 - - - +
43Z VAL* 3.5 5.1 - - - +
44Z ASN* 3.0 32.5 + - + +
46Z PHE* 4.0 30.1 - - - -
82Z THR* 4.5 2.9 - - - -
83Z ASP* 1.3 75.0 - - - +
85Z ARG* 1.3 61.5 + - - +
97Z TYR* 4.0 13.0 - - + -
98Z ARG 3.1 4.9 - - - -
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Residues in contact with ARG 85 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320Y LYS* 5.9 6.7 - - - +
349Y ASN* 4.6 7.4 - - - +
378Y ASP* 4.4 14.5 + - - -
406Y ASN* 5.9 0.6 - - - +
42Z PRO 3.4 8.5 - - - +
43Z VAL* 3.7 32.6 - - + +
83Z ASP* 5.7 5.5 - - + +
84Z CYS* 1.3 75.9 - - - +
86Z LEU* 1.3 73.7 - - + +
97Z TYR* 3.4 4.4 - - - -
98Z ARG* 2.6 85.3 + - + +
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Residues in contact with LEU 86 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320Y LYS* 5.3 10.0 + - + +
40Z CYS* 3.5 37.2 - - + +
41Z LYS 4.3 0.9 - - - +
42Z PRO* 2.9 30.5 + - + +
85Z ARG* 1.3 80.0 - - + +
87Z THR* 1.3 66.4 + - - +
88Z ASN* 3.8 6.7 + - - +
90Z SER* 3.6 29.2 - - - +
95Z CYS* 4.3 1.6 - - + -
96Z ALA 3.7 10.5 - - - +
97Z TYR* 3.6 16.4 - - + -
98Z ARG* 5.4 0.3 - - - +
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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