Contacts of the strand formed by residues 74 - 80 (chain F) in PDB entry 2C2V
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 ARG 74 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C GLU* 5.2 5.3 + - - -
74C ARG* 3.1 53.7 - - - +
64F LEU* 3.6 9.9 - - - +
65F GLU* 3.0 46.5 + - + +
66F ASP* 4.0 1.8 + - + +
69F ASP* 3.9 12.8 + - + +
71F THR* 4.9 2.0 + - - -
72F LEU 3.6 0.4 - - - -
73F THR* 1.3 100.2 - - + +
75F TRP* 1.3 66.2 - - - +
95F LYS* 4.8 4.9 - - - +
96F ILE 3.6 2.5 - - - +
97F GLU* 4.5 21.5 + - + +
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Residues in contact with TRP 75 (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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44F LEU* 3.8 27.7 - - + +
47F GLU* 4.4 2.2 - - + -
48F LEU* 3.8 40.6 - - + -
62F TRP* 4.1 11.4 - + - -
63F GLY* 3.2 39.0 - - - -
64F LEU* 3.7 15.7 - - + -
65F GLU* 4.0 6.8 + - - +
72F LEU* 3.3 23.0 + - + -
73F THR 3.3 13.7 - - - -
74F ARG* 1.3 82.3 - - - +
76F THR* 1.3 56.9 + - - +
95F LYS* 3.3 5.0 - - - +
96F ILE* 2.4 58.9 + - + +
98F CYS* 4.0 17.9 - - - -
144F ILE* 3.3 26.9 - - + -
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Residues in contact with THR 76 (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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62F TRP* 3.1 5.5 - - - +
63F GLY 2.8 32.9 + - - -
64F LEU 4.7 1.0 - - - -
65F GLU* 4.1 20.7 + - - +
75F TRP* 1.3 73.7 - - - +
77F GLY* 1.3 78.3 + - - +
78F MET* 5.1 4.3 - - + -
93F SER* 5.4 4.7 - - - +
94F LEU 3.3 9.0 - - - +
95F LYS* 4.7 2.4 - - - +
96F ILE* 3.7 3.8 - - - -
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Residues in contact with GLY 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 SER 3.3 11.4 - - - -
62F TRP* 4.2 1.1 - - - -
76F THR* 1.3 84.8 - - - +
78F MET* 1.4 61.6 + - - +
93F SER* 3.4 3.5 - - - -
94F LEU* 2.6 48.9 + - - -
96F ILE* 3.4 13.4 - - - +
148F LEU* 4.4 3.1 - - - -
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Residues in contact with MET 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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58F GLY 4.4 8.1 - - - +
60F VAL* 3.5 2.1 - - - +
61F SER* 3.2 51.8 + - - +
76F THR* 5.1 4.5 - - + -
77F GLY* 1.4 75.4 - - - +
79F ILE* 1.4 70.8 + - - +
80F LEU* 3.5 35.0 - - + -
91F ILE* 3.8 26.5 - - + -
92F TYR 3.3 6.5 - - - +
93F SER* 4.9 5.6 - - - +
94F LEU* 3.7 1.0 - - - +
148F LEU* 4.4 0.9 - - - +
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Residues in contact with ILE 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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59F THR 3.7 4.0 - - - -
60F VAL* 4.8 2.7 - - + -
78F MET* 1.4 79.5 - - - +
80F LEU* 1.3 69.6 + - - +
81F GLY 3.5 0.2 + - - -
90F ARG 3.4 1.0 - - - +
92F TYR* 2.8 40.9 + - + +
94F LEU* 3.7 25.6 - - + -
111F PHE* 4.7 5.8 - - + -
148F LEU* 4.0 22.7 - - + +
151F LEU* 3.9 28.7 - - + -
152F ARG* 4.3 14.4 - - + +
155F MET* 3.9 27.6 - - + -
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Residues in contact with LEU 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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58F GLY 3.7 15.3 - - - +
59F THR* 2.9 34.7 + - - +
78F MET* 3.5 31.6 - - + -
79F ILE* 1.3 73.1 - - - +
81F GLY* 1.3 78.0 + - - +
82F PRO* 2.8 5.9 - - - +
89F ASN* 5.1 5.6 - - - +
90F ARG 3.8 9.4 - - - +
91F ILE* 4.4 15.9 - - + -
152F ARG* 3.3 13.0 + - - +
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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