Contacts of the strand formed by residues 96 - 103 (chain C) in PDB entry 6PB4
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 LEU 96 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C PHE* 5.9 3.6 - - + -
73C TYR* 5.0 5.8 - - + -
74C ARG 3.7 0.9 - - - +
75C LEU* 3.5 21.5 - - + -
94C ALA 3.4 2.4 + - - -
95C PRO* 1.3 72.7 - - - +
97C ARG* 1.3 75.0 + - - +
98C VAL* 3.5 26.0 - - + -
123C TYR* 2.9 25.7 - - - -
124C MET* 2.9 38.8 + - + +
125C GLY* 3.0 19.1 + - - +
127C ILE* 4.5 12.8 - - + -
464C PHE* 5.2 14.8 - - + -
498C ILE* 6.3 1.8 - - + -
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Residues in contact with ARG 97 (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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74C ARG* 2.6 80.9 + - - +
75C LEU* 3.7 19.6 + - - +
76C GLY* 4.2 8.9 - - - +
95C PRO* 4.1 4.3 - - + +
96C LEU* 1.3 79.1 - - - +
98C VAL* 1.3 64.5 + - - +
121C GLU* 2.4 42.2 + - - +
122C VAL 3.0 17.7 - - - +
123C TYR* 3.7 19.7 - - + +
124C MET 4.7 0.2 - - - +
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Residues in contact with VAL 98 (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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53C PHE* 5.0 11.9 - - + -
70C TYR* 4.1 18.2 - - + -
72C SER 3.3 14.4 - - - +
73C TYR* 4.2 8.1 - - + +
96C LEU* 3.5 20.4 - - + -
97C ARG* 1.3 81.4 - - - +
99C LYS* 1.3 72.2 + - - +
100C LEU* 3.8 4.7 - - + +
121C GLU* 3.5 4.4 - - - -
122C VAL* 2.9 32.9 + - + +
124C MET* 3.7 30.3 - - + -
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Residues in contact with LYS 99 (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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70C TYR* 4.6 1.4 - - - -
71C VAL* 3.4 41.4 + - + +
72C SER* 2.8 33.9 + - - +
73C TYR* 5.5 1.6 - - - -
74C ARG* 3.6 28.2 - - - +
98C VAL* 1.3 80.8 - - - +
100C LEU* 1.3 62.0 + - - +
119C GLU* 4.6 3.8 - - - +
120C GLN 3.7 5.2 - - - +
121C GLU* 3.4 35.0 - - + +
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Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 6.2 4.0 - - + -
69C GLN 3.6 9.9 - - - +
70C TYR* 5.5 0.4 - - - -
71C VAL* 3.4 10.5 - - - +
98C VAL* 3.8 6.5 - - + +
99C LYS* 1.3 75.4 - - - +
101C ARG* 1.3 61.8 + - - +
118C LYS 3.5 0.2 - - - +
119C GLU* 3.4 1.9 - - - -
120C GLN* 2.7 58.3 + - + +
121C GLU* 3.8 3.1 - - - -
122C VAL* 3.3 35.0 - - + -
489C PRO* 3.6 30.1 - - + -
493C ILE* 4.5 9.4 - - + -
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Residues in contact with ARG 101 (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 LEU* 4.7 0.7 - - - -
69C GLN* 2.4 68.8 + - - +
70C TYR 3.4 10.3 + - - -
71C VAL* 3.4 23.2 - - + +
100C LEU* 1.3 76.6 - - - +
102C LEU* 1.3 60.2 + - - +
103C VAL* 3.0 19.3 + - + +
117C ILE* 3.3 32.5 - - + -
118C LYS 3.5 2.2 - - - -
119C GLU* 3.4 17.9 - - + +
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Residues in contact with LEU 102 (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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67C GLU 3.8 14.8 - - - +
68C LEU* 4.2 16.4 - - + +
100C LEU 4.2 0.2 - - - -
101C ARG* 1.3 67.7 - - - +
103C VAL* 1.3 52.6 + - - +
104C ILE* 3.3 14.0 - - + +
116C ASP* 2.7 41.1 - - - +
117C ILE* 3.3 7.5 - - - -
118C LYS* 2.9 26.9 + - + +
479C LEU* 5.6 5.4 - - + -
484C LEU 5.4 0.9 - - - +
487C LEU 3.0 28.5 - - - +
488C MET 5.1 0.4 - - - +
489C PRO* 3.4 38.5 - - + +
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C GLU* 2.7 40.5 + - - +
68C LEU* 4.2 0.2 - - - +
69C GLN* 3.3 26.5 - - - +
101C ARG* 3.0 41.6 + - + +
102C LEU* 1.3 71.0 - - - +
104C ILE* 1.3 63.5 + - - +
105C TYR* 3.0 37.2 - - + +
113C THR* 4.5 2.5 - - - +
116C ASP 3.5 2.2 - - - -
117C ILE* 4.0 19.3 - - + -
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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