Contacts of the strand formed by residues 80 - 87 (chain C) in PDB entry 4IHB
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 PHE 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68C VAL* 3.7 31.4 - - + -
69C VAL 4.3 2.0 - - - -
70C LYS* 4.3 13.2 - - - +
78C ASN* 3.5 5.1 - - - +
79C ARG* 1.3 76.7 - - - +
81C LEU* 1.3 67.9 + - - +
82C GLY* 3.6 19.7 - - - -
83C GLU* 3.4 42.0 - - + -
106C LEU 3.9 1.3 - - - -
107C ASP* 3.7 4.9 - - + -
108C THR* 3.5 35.7 - - + -
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Residues in contact with LEU 81 (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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12C VAL* 3.6 30.1 - - + -
13C HIS 4.3 8.0 - - - +
14C THR* 3.6 38.4 - - + -
15C PRO* 4.8 3.6 - - + -
20C SER* 4.7 0.7 - - - -
22C ALA* 4.7 2.5 - - + -
69C VAL* 3.0 20.3 + - + +
70C LYS 3.9 5.6 - - - +
71C ASP* 3.6 25.6 - - + +
78C ASN 3.9 12.8 - - - +
79C ARG 3.9 0.4 - - - +
80C PHE* 1.3 89.5 - - - +
82C GLY* 1.3 60.9 + - - +
105C LEU* 5.9 0.7 - - - -
107C ASP* 4.9 1.0 - - - +
113C THR* 3.6 22.2 + - - +
115C ALA* 5.9 0.7 - - - +
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Residues in contact with GLY 82 (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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68C VAL* 3.5 2.4 - - - +
69C VAL* 2.8 29.3 + - - +
80C PHE* 3.6 9.9 - - - -
81C LEU* 1.3 81.4 - - - +
83C GLU* 1.3 62.1 + - - +
105C LEU* 4.2 20.0 - - - -
106C LEU 3.2 15.0 - - - -
113C THR* 4.6 0.2 - - - -
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Residues in contact with GLU 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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66C HIS* 2.5 35.4 + - - +
67C VAL 3.2 12.1 - - - +
68C VAL* 3.7 10.0 - - + +
80C PHE* 3.4 25.1 - - + -
82C GLY* 1.3 75.6 - - - +
84C ALA* 1.3 62.9 + - - +
85C LYS* 5.3 5.0 - - + +
104C PRO 4.3 0.2 - - - +
105C LEU* 3.7 5.7 - - - +
106C LEU* 2.8 42.7 + - + +
107C ASP 4.2 0.2 - - - +
108C THR* 4.9 1.9 - - - -
110C LYS* 2.8 31.9 + - - +
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Residues in contact with ALA 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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65C LEU 3.8 1.0 - - - +
66C HIS* 3.8 3.5 - - - -
67C VAL* 2.8 40.1 + - + +
83C GLU* 1.3 75.4 - - - +
85C LYS* 1.3 65.3 + - - +
86C VAL* 4.0 6.0 - - + +
103C ALA* 4.1 24.9 - - + -
104C PRO 4.4 4.9 - - - +
105C LEU* 4.0 15.7 - - + +
106C LEU* 6.0 0.4 - - - -
117C LEU* 5.1 4.3 - - + -
119C LEU* 6.0 0.4 - - + -
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Residues in contact with LYS 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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64C GLU* 4.1 35.4 + - + +
65C LEU 3.6 4.0 - - - +
66C HIS* 3.9 38.9 + - + +
83C GLU* 5.3 3.4 - - + +
84C ALA* 1.3 76.0 - - - +
86C VAL* 1.3 62.2 + - - +
87C PRO* 3.2 12.7 - - - +
110C LYS* 6.2 5.2 - - - +
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Residues in contact with VAL 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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64C GLU* 3.4 3.5 - - - +
65C LEU* 2.8 50.8 + - + +
67C VAL* 5.1 2.9 - - + -
84C ALA* 4.9 9.2 - - + +
85C LYS* 1.3 73.7 - - - +
87C PRO* 1.3 67.4 - - - +
88C LEU* 3.4 8.0 + - + +
101C PHE* 3.5 45.3 - - + -
103C ALA* 5.7 2.9 - - + -
119C LEU* 4.2 30.1 - - + -
121C VAL* 4.6 7.9 - - + -
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Residues in contact with PRO 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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61C GLN* 2.8 18.8 - - + +
64C GLU* 3.6 18.8 - - + +
85C LYS 3.2 12.1 - - - +
86C VAL* 1.3 91.0 - - + +
88C LEU* 1.3 58.9 + - - +
89C ARG* 4.0 19.5 - - - +
90C GLU* 3.2 46.8 - - - +
91C VAL* 4.1 1.0 + - - +
101C PHE* 5.1 2.7 - - + -
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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