Contacts of the strand formed by residues 79 - 86 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47X VAL* 4.1 16.6 - - + -
49X GLU* 3.6 26.5 - - + -
53X ASP* 3.5 45.1 - - + +
54X VAL* 4.0 4.5 - - + +
57X VAL* 4.2 8.5 - - + -
60X GLN* 5.8 0.9 - - - +
75X SER* 4.2 7.2 - - - +
77X SER* 3.2 15.2 + - - +
78X SER* 1.3 74.6 - - - +
80X HIS* 1.3 62.7 + - - +
81X ILE* 3.3 7.7 + - + +
103X GLU* 3.2 2.5 - - - -
104X ARG 2.6 36.6 + - - +
106X ILE* 4.0 28.9 - - + -
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Residues in contact with HIS 80 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X PRO* 4.3 29.0 - - + +
47X VAL* 4.5 0.3 - - - +
48X HIS* 2.7 48.4 + - + -
49X GLU* 3.0 26.5 + - - +
78X SER 5.2 4.1 + - - -
79X MET* 1.3 72.7 - - - +
81X ILE* 1.3 55.7 + - - +
102X LYS 3.5 6.1 - - - +
103X GLU* 3.1 38.9 - - + +
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Residues in contact with ILE 81 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19X PRO 5.1 0.3 - - - +
45X THR* 3.5 20.4 - - + -
46X PHE 3.2 14.1 - - - +
47X VAL* 4.2 11.2 - - + -
48X HIS* 3.8 3.2 - - - -
79X MET* 3.3 13.4 + - + +
80X HIS* 1.3 79.8 - - - +
82X THR* 1.3 62.5 + - - +
83X ASP* 3.7 10.5 - - - +
101X PRO* 3.4 1.2 - - - +
102X LYS* 2.7 57.9 + - + +
104X ARG* 4.3 6.7 - - + +
106X ILE* 4.1 22.9 - - + -
120X PHE* 5.0 0.4 - - + -
123X SER* 3.6 29.8 - - - +
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Residues in contact with THR 82 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X SER* 2.6 24.6 + - - +
25X TYR* 4.0 15.7 - - + -
26X CYS* 4.1 3.4 - - - -
44X ASN 4.1 0.2 - - - +
45X THR* 3.5 3.7 - - - -
46X PHE* 3.0 28.9 + - - +
48X HIS* 2.7 20.2 + - - -
81X ILE* 1.3 77.1 + - - +
83X ASP* 1.3 68.8 + - - +
84X CYS* 3.9 2.6 + - - -
99X THR* 3.4 33.0 - - + -
100X SER 3.3 9.2 - - - +
101X PRO* 3.7 5.5 - - - +
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Residues in contact with ASP 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X CYS* 3.7 0.9 - - - -
43X VAL* 5.8 5.2 - - + -
44X ASN 3.9 2.0 - - - -
45X THR* 2.8 33.2 + - - +
81X ILE* 3.7 4.8 - - - +
82X THR* 1.3 73.5 - - - +
84X CYS* 1.3 63.5 + - - +
85X ARG* 4.1 12.7 + - - +
98X ARG* 3.5 3.6 - - - +
99X THR* 3.5 1.6 - - - -
100X SER* 2.6 50.3 + - - +
102X LYS* 2.7 39.4 + - - +
123X SER* 4.4 7.9 + - - -
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Residues in contact with CYS 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26X CYS* 2.0 54.5 - - + -
30X MET* 4.2 9.2 - - + -
42X PRO 4.2 0.2 - - - +
43X VAL* 3.5 11.9 - - - +
44X ASN 3.0 33.5 + - - +
46X PHE* 3.9 30.1 - - - -
82X THR* 4.5 2.5 - - - -
83X ASP* 1.3 73.8 - - - +
85X ARG* 1.3 60.5 + - - +
97X TYR* 4.1 12.5 - - + -
98X ARG 3.3 1.1 - - - -
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Residues in contact with ARG 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349W ASN* 6.0 2.0 - - - +
42X PRO 4.3 1.8 - - - +
43X VAL* 5.1 16.7 - - + +
83X ASP* 4.1 15.4 + - + +
84X CYS* 1.3 73.5 - - - +
86X LEU* 1.3 73.3 + - - +
87X THR 3.4 0.3 + - - -
97X TYR* 3.1 5.1 - - - -
98X ARG* 2.7 90.6 + - - +
102X LYS* 5.5 3.6 - - - +
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Residues in contact with LEU 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320W LYS* 4.4 19.6 + - - +
40X CYS* 4.1 20.6 - - + +
42X PRO* 3.1 40.0 + - + +
85X ARG* 1.3 81.8 - - - +
87X THR* 1.3 70.0 + - - +
88X ASN* 3.7 5.5 + - - +
90X SER* 3.6 17.3 - - - +
96X ALA 3.4 19.7 - - - +
97X TYR* 3.7 27.0 - - + +
98X ARG* 5.5 0.7 + - - -
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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