Contacts of the strand formed by residues 76 - 86 (chain H) in PDB entry 2QC8
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 ASP 76 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H ASN* 4.5 16.0 + - + +
62H PHE 3.4 8.1 - - - +
74H ASN 4.3 0.5 - - - +
75H SER* 1.3 75.5 - - - +
77H MET* 1.3 62.7 + - - +
104H TYR* 4.4 4.9 - - - +
317I ALA* 3.6 16.0 - - - +
319I ARG* 2.8 18.9 + - - +
324I ARG* 3.2 28.7 + - - -
326I PRO* 3.7 1.6 - - - +
327I ARG* 2.8 68.1 + - + +
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Residues in contact with MET 77 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61H ASN* 2.9 26.7 - - - -
62H PHE* 3.0 31.8 + - + +
64H GLY* 3.8 11.0 - - - -
69H GLN* 3.4 42.8 - - + +
70H SER* 3.9 6.1 - - - +
75H SER 3.5 9.0 - - - +
76H ASP* 1.3 78.9 - - - +
78H TYR* 1.3 65.3 + - - +
101H VAL* 3.5 23.1 - - + -
102H PHE 3.4 12.1 - - - +
103H LYS* 3.8 20.6 - - + -
104H TYR 5.0 1.3 - - - +
109H ALA* 3.9 13.7 - - + -
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Residues in contact with TYR 78 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H GLU* 3.7 18.4 - - - -
60H TRP 3.6 9.9 - - - +
61H ASN* 4.4 2.7 - - + -
62H PHE* 4.0 0.3 - - - -
77H MET* 1.3 76.1 - - - +
79H LEU* 1.3 66.2 + - - +
80H VAL* 4.1 4.9 - - + -
101H VAL* 3.5 9.9 - - - +
102H PHE* 3.0 45.9 + - + +
103H LYS 3.4 25.6 - - - -
104H TYR 3.9 9.3 + - - -
106H ARG* 3.4 49.4 + - + +
327I ARG* 3.3 28.9 - - + -
328I THR* 5.8 6.5 - - - -
331I GLN* 4.0 18.8 + - + +
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Residues in contact with LEU 79 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H TYR* 4.3 18.4 - - + -
32H TRP* 3.7 57.7 - - + -
43H LYS* 4.6 3.8 - - - -
59H GLU* 3.4 9.2 - - - +
60H TRP* 3.0 38.5 + - + +
61H ASN* 3.9 18.2 - - - +
62H PHE* 3.7 29.2 - - + -
78H TYR* 1.3 72.1 - - - +
80H VAL* 1.3 62.6 + - - +
81H PRO* 3.5 2.6 - - - +
99H CYS* 3.8 20.4 - - + -
100H GLU 3.7 1.1 - - - +
101H VAL* 4.3 3.6 - - + -
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Residues in contact with VAL 80 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H GLU* 3.8 26.5 - - + +
78H TYR* 4.9 5.2 - - + -
79H LEU* 1.3 75.5 - - - +
81H PRO* 1.3 81.1 - - + +
82H ALA* 3.4 1.2 + - - +
99H CYS* 3.4 2.8 - - - +
100H GLU* 3.1 30.7 + - + +
102H PHE* 4.0 32.3 - - + -
106H ARG* 5.4 4.0 - - - +
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Residues in contact with PRO 81 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30H TYR* 4.1 11.0 - - + -
54H VAL* 3.7 29.6 - - + +
57H LEU* 3.6 19.5 - - + +
58H PRO 3.4 24.5 - - - +
59H GLU* 4.1 5.6 - - + +
79H LEU 3.5 10.1 - - - +
80H VAL* 1.3 94.6 - - + +
82H ALA* 1.3 59.2 + - - +
97H VAL* 3.8 15.5 - - + -
98H LEU 3.9 1.6 - - - +
99H CYS* 3.9 2.0 - - - -
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Residues in contact with ALA 82 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H VAL* 3.8 17.7 - - - +
80H VAL 3.4 7.1 + - - +
81H PRO* 1.3 74.3 - - - +
83H ALA* 1.3 60.5 + - + +
98H LEU* 2.7 20.2 + - + +
99H CYS* 4.3 3.1 - - - -
100H GLU* 4.4 3.8 - - + +
114H ARG* 3.5 47.2 + - - +
216H ASP* 4.8 0.7 - - - +
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Residues in contact with ALA 83 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54H VAL* 4.2 5.4 - - - -
82H ALA* 1.3 80.7 - - - +
84H MET* 1.3 60.3 + - - +
85H PHE* 4.1 18.1 - - + -
96H LEU 3.9 0.3 - - - +
97H VAL* 3.4 1.8 - - - -
98H LEU* 2.7 38.9 + - + +
216H ASP* 3.9 33.9 - - + +
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Residues in contact with MET 84 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H PRO* 3.8 17.0 - - - +
52H LYS* 3.5 29.2 - - - +
53H CYS* 3.6 17.7 - - - +
54H VAL* 3.7 19.7 - - + +
57H LEU* 3.8 22.7 - - + -
83H ALA* 1.3 71.2 - - - +
85H PHE* 1.3 85.0 + - - +
95H LYS* 4.0 28.3 - - + -
96H LEU 3.4 8.5 - - - +
97H VAL* 4.5 0.9 - - - +
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Residues in contact with PHE 85 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H ALA* 4.1 20.6 - - + -
84H MET* 1.3 85.7 - - - +
86H ARG* 1.3 65.2 + - - +
95H LYS* 3.3 10.7 - - - +
96H LEU* 2.7 47.3 + - + +
186H ALA* 3.5 19.7 - - + +
187H GLY* 3.5 28.5 - - - -
188H VAL* 3.8 12.6 - - + -
216H ASP 4.4 0.9 - - - -
217H HIS* 3.7 35.7 - + - -
220H VAL* 3.5 37.9 - - + -
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Residues in contact with ARG 86 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21G PRO* 5.1 5.1 + - - +
22G GLN 5.9 0.8 + - - -
85H PHE* 1.3 77.3 - - - +
87H ASP* 1.3 58.2 + - - +
88H PRO* 3.3 12.4 - - - +
92H ASP* 2.4 42.6 + - - +
94H ASN 3.9 5.8 - - - -
95H LYS* 4.6 10.1 - - - +
96H LEU* 4.0 3.0 - - - +
184H LEU 5.0 1.0 + - - -
185H TYR* 3.1 64.8 + - + +
186H ALA* 3.0 25.0 + - - +
187H GLY* 5.7 0.9 - - - -
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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