Contacts of the strand formed by residues 82 - 87 (chain C) in PDB entry 3C3P
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 82 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLN 2.9 10.4 + - - +
58C LEU* 3.5 16.2 - - + +
59C VAL* 2.9 26.9 + - - +
77C ILE* 3.7 6.1 - - - +
79C ILE* 2.6 30.1 + - - +
80C SER* 3.7 9.4 + - - +
81C SER* 1.3 97.2 + - - +
83C VAL* 1.3 63.1 + - - +
84C VAL* 4.1 4.9 - - + -
107C ASP 3.9 18.8 + - - -
108C ARG* 3.3 17.4 - - - +
109C VAL* 4.6 4.3 - - - +
110C GLU* 5.3 7.0 - - + +
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C VAL* 3.3 13.7 - - + +
61C VAL* 4.0 25.1 - - + -
70C SER* 4.1 22.2 - - - +
73C PHE* 4.0 9.9 - - + -
74C ALA* 3.9 24.9 - - + +
77C ILE* 3.5 22.0 - - + -
82C ARG* 1.3 74.5 - - - +
84C VAL* 1.3 58.6 + - - +
85C MSE 4.0 0.2 - - - -
108C ARG 3.0 7.7 + - - +
109C VAL* 3.3 15.3 - - + +
110C GLU* 2.8 32.4 + - - +
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C LEU* 3.8 22.4 - - + -
59C VAL 2.8 11.8 + - - +
60C VAL* 3.4 10.3 - - + +
61C VAL* 2.7 32.9 + - - +
82C ARG* 4.9 4.5 - - + -
83C VAL* 1.3 75.9 - - - +
85C MSE 1.3 58.3 + - - +
86C ILE* 4.0 19.7 - - + +
110C GLU* 3.4 38.8 - - + +
112C GLN* 4.5 7.4 - - - +
119C ILE* 5.7 0.4 - - + -
123C GLN* 3.8 23.1 - - + +
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Residues in contact with MSE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 3.4 9.6 - - + +
64C ASP* 3.9 16.8 - - + +
67C GLY* 3.8 18.4 - - - -
70C SER* 3.3 26.0 - - - +
83C VAL* 4.0 3.1 - - + -
84C VAL* 1.3 74.3 - - - +
86C ILE* 1.3 81.0 - - - +
87C ASP* 4.0 12.3 - - - -
92C ASN 4.3 6.3 - - - +
93C VAL* 4.1 12.1 - - - -
96C ALA* 3.6 31.4 - - + -
110C GLU 2.9 9.6 + - - +
111C LEU* 3.4 22.1 - - + -
112C GLN* 2.9 26.9 + - - +
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Residues in contact with ILE 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C VAL* 4.3 12.3 - - + -
61C VAL 3.0 14.2 + - - +
62C PRO* 4.4 1.8 - - + -
63C GLY* 2.6 35.5 + - - -
84C VAL* 4.0 21.1 - - + +
85C MSE 1.3 82.8 - - - +
87C ASP* 1.3 62.7 + - - +
112C GLN* 3.4 13.2 - - + +
114C GLY 3.6 14.8 - - - +
116C PRO* 3.7 28.4 - - + +
119C ILE* 3.5 44.2 - - + -
120C ALA* 4.2 10.1 - - + +
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Residues in contact with ASP 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C GLY* 3.6 4.3 - - - -
64C ASP 3.0 24.2 + - - +
65C GLY 4.3 0.3 + - - -
85C MSE 4.0 14.1 - - - -
86C ILE* 1.3 75.3 - - - +
88C PRO* 1.3 73.5 - - - +
89C ASP* 2.9 25.2 + - - +
92C ASN* 2.8 35.2 + - + +
93C VAL* 4.1 10.9 - - + +
112C GLN 3.1 6.3 + - - -
113C VAL* 3.2 9.0 - - - +
114C GLY 2.8 20.7 + - - -
211C EDO 4.9 4.7 - - - -
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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