Contacts of the strand formed by residues 76 - 86 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61F ASN* 4.3 16.5 + - + +
62F PHE 3.4 8.3 - - - -
70F SER* 5.2 0.2 - - - -
74F ASN 4.1 1.7 - - - +
75F SER* 1.3 75.2 - - - +
77F MET* 1.3 61.1 + - - +
104F TYR* 4.4 5.9 + - - +
317G ALA* 3.7 14.7 - - - +
319G ARG* 3.1 17.5 + - - +
324G ARG* 3.2 29.5 + - - -
326G PRO* 3.7 0.7 - - - +
327G ARG* 2.9 68.5 + - + +
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Residues in contact with MET 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F ASN* 2.9 9.0 - - - +
62F PHE* 2.9 49.2 + - + +
64F GLY* 3.7 13.9 - - - -
69F GLN* 3.4 42.8 - - + +
70F SER* 3.9 6.3 - - - +
75F SER 3.4 13.9 - - - +
76F ASP* 1.3 74.6 - - - +
78F TYR* 1.3 64.1 + - - +
101F VAL* 3.5 16.4 - - + -
102F PHE 3.4 19.7 - - - +
103F LYS* 3.8 19.1 - - + -
104F TYR 5.3 0.7 - - - +
109F ALA* 4.0 11.2 - - + -
110F GLU* 5.8 0.2 - - - +
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Residues in contact with TYR 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F GLU* 3.7 18.4 - - - -
60F TRP 3.6 7.9 - - - -
61F ASN* 4.3 3.4 - - + +
77F MET* 1.3 76.3 - - - +
79F LEU* 1.3 65.4 + - - +
80F VAL* 4.1 3.6 - - + -
100F GLU 3.6 0.4 - - - +
101F VAL* 3.3 12.8 - - - +
102F PHE* 3.0 45.4 + - + +
103F LYS 3.3 26.9 - - - -
104F TYR 3.9 6.0 + - - -
106F ARG* 3.5 45.5 + - + +
327G ARG* 3.4 39.0 - - + +
328G THR* 5.6 6.5 - - - -
331G GLN* 3.9 17.2 - - + +
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Residues in contact with LEU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F TYR* 4.2 10.9 - - + -
32F TRP* 3.4 58.6 - - + -
43F LYS* 4.7 3.4 - - - -
59F GLU* 3.5 7.6 - - - +
60F TRP* 2.8 38.8 + - + +
61F ASN 3.6 22.4 - - - +
62F PHE* 3.6 29.2 - - + -
78F TYR* 1.3 72.5 - - - +
80F VAL* 1.3 62.8 + - - +
81F PRO* 3.6 2.8 - - - +
99F CYS* 4.0 19.3 - - + -
100F GLU 3.6 1.8 - - - -
101F VAL* 4.3 3.8 - - + -
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Residues in contact with VAL 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F GLU* 4.1 24.9 - - + +
78F TYR* 4.9 5.4 - - + -
79F LEU* 1.3 74.3 - - - +
81F PRO* 1.4 80.9 - - + +
82F ALA* 3.3 1.0 + - - +
99F CYS* 3.3 3.0 - - - +
100F GLU* 3.1 31.4 + - + +
102F PHE* 3.7 34.1 - - + -
106F ARG* 5.6 4.0 - - - +
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Residues in contact with PRO 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F TYR* 4.1 11.9 - - + -
54F VAL* 3.8 27.6 - - + +
57F LEU* 3.7 20.6 - - + +
58F PRO 3.6 23.3 - - - +
59F GLU* 4.2 5.8 - - + +
79F LEU 3.6 9.4 - - - +
80F VAL* 1.4 97.6 - - + +
82F ALA* 1.3 59.3 + - - +
97F VAL* 3.9 8.7 - - + -
98F LEU 3.8 7.0 - - - +
99F CYS* 4.1 4.3 - - - -
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Residues in contact with ALA 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F VAL* 3.7 15.1 - - - +
80F VAL 3.3 5.4 + - - +
81F PRO* 1.3 74.4 - - - +
83F ALA* 1.3 62.5 + - + +
98F LEU* 2.8 19.6 + - + +
99F CYS 4.4 0.7 - - - -
100F GLU* 4.3 11.2 - - + +
114F ARG* 3.7 42.5 + - - +
216F ASP* 5.0 0.6 - - - +
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Residues in contact with ALA 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54F VAL* 3.8 7.0 - - - -
82F ALA* 1.3 81.1 - - - +
84F MET* 1.3 61.4 + - - +
85F PHE* 4.0 22.1 - - + -
96F LEU 3.9 0.5 - - - +
97F VAL* 3.3 3.0 - - - -
98F LEU* 2.7 42.6 + - + +
216F ASP* 4.1 25.8 - - + +
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Residues in contact with MET 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F PRO* 3.7 26.0 - - - +
52F LYS 3.6 31.6 - - - +
53F CYS* 4.0 10.5 - - - +
54F VAL* 3.8 20.2 - - + +
57F LEU* 3.7 25.1 - - + -
83F ALA* 1.3 73.3 - - - +
85F PHE* 1.3 81.9 + - - +
95F LYS* 4.0 20.0 - - + +
96F LEU 3.3 9.6 - - - +
97F VAL* 4.4 0.4 - - - +
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Residues in contact with PHE 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F ALA* 4.0 26.2 - - + -
84F MET* 1.3 82.9 - - - +
86F ARG* 1.3 65.5 + - - +
95F LYS* 3.4 10.4 - - - +
96F LEU* 2.7 38.8 + - + +
186F ALA* 3.3 23.1 - - + +
187F GLY* 3.6 24.0 - - - -
188F VAL* 4.0 10.1 - - + -
216F ASP 4.6 2.0 - - - -
217F HIS* 3.6 40.6 - + - -
220F VAL* 3.6 36.3 - - + -
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Residues in contact with ARG 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F PHE* 1.3 77.7 - - - +
87F ASP* 1.3 60.1 + - - +
88F PRO* 3.2 12.6 - - - +
92F ASP* 2.7 40.4 + - - +
94F ASN 4.0 4.5 - - - -
95F LYS* 4.7 11.4 - - - +
96F LEU* 4.2 2.2 - - - +
184F LEU 5.1 1.4 + - - -
185F TYR* 2.9 66.1 + - + +
186F ALA* 3.1 21.9 + - - +
187F GLY* 5.8 0.7 - - - -
21J PRO* 5.0 5.5 + - - +
22J GLN 6.2 0.4 - - - -
23J GLY* 6.0 4.2 - - - -
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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