Contacts of the strand formed by residues 106 - 112 (chain F) in PDB entry 1VCB
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 GLY 106 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ILE* 5.7 1.1 - - - -
76F PHE 3.0 13.7 - - - -
77F CYS* 4.0 12.3 - - - -
101F LEU* 4.1 4.0 - - - +
105F THR* 1.3 79.3 - - - +
107F ARG* 1.3 63.0 + - - +
109H PHE* 2.9 29.3 - - - -
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Residues in contact with ARG 107 (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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75F ILE* 3.5 3.8 - - - +
76F PHE* 2.8 39.8 + - + +
86F PRO* 5.6 1.0 - - - +
99F PRO* 3.0 45.0 + - - +
100F THR 3.1 21.2 + - - -
101F LEU* 3.7 24.6 - - + +
102F PRO* 4.5 5.7 - - - +
106F GLY* 1.3 76.4 - - - +
108F ARG* 1.3 62.9 + - - +
109F ILE* 3.5 27.4 + - + +
109H PHE* 3.4 11.6 - - + -
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Residues in contact with ARG 108 (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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73F GLN* 3.0 46.9 - - + +
74F VAL 3.5 10.5 - - - +
75F ILE* 4.4 7.6 - - + +
107F ARG* 1.3 76.0 - - - +
109F ILE* 1.3 69.8 + - - +
110F HIS* 3.7 21.6 + - - -
146F PRO* 5.7 6.1 - - + -
41H THR* 4.0 10.5 - - - +
108H ASN* 3.3 31.9 + - - +
109H PHE* 4.1 16.0 + - + +
111H ASP* 3.4 39.7 + - - +
159I LYS* 5.6 4.9 - - - +
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Residues in contact with ILE 109 (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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73F GLN* 3.7 7.0 - - - +
74F VAL* 2.6 43.7 + - + +
76F PHE* 3.5 48.2 - - + -
98F TYR* 5.8 8.3 - - + -
107F ARG* 3.5 30.1 - - + +
108F ARG* 1.3 85.7 - - - +
110F HIS* 1.3 76.3 + - - +
111F SER* 4.5 4.5 - - - +
117F TRP* 4.4 15.5 - - + -
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Residues in contact with HIS 110 (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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72F SER 4.2 2.7 - - - -
73F GLN* 3.5 32.0 + - + -
98F TYR* 6.1 0.7 - - - -
108F ARG* 3.7 20.6 + - - -
109F ILE* 1.3 82.0 - - - +
111F SER* 1.3 61.6 + - - +
112F TYR* 4.8 9.0 - - + +
117F TRP* 5.4 1.6 - - - -
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Residues in contact with SER 111 (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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71F PRO* 3.6 4.2 - - - +
72F SER 2.9 30.6 + - - -
74F VAL* 4.2 7.9 - - - -
109F ILE* 3.9 6.5 + - - -
110F HIS* 1.3 76.3 - - - +
112F TYR* 1.3 86.1 + - - +
115F HIS* 3.8 8.9 + - - +
117F TRP* 3.2 30.5 + - - -
138F PRO* 3.4 18.3 - - - +
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Residues in contact with TYR 112 (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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68F SER 3.7 13.5 - - - +
69F ARG* 3.7 18.8 - - + -
70F GLU 3.1 28.5 - - - +
71F PRO* 3.6 19.7 - - + -
72F SER* 3.7 7.8 + - - +
110F HIS* 4.8 8.0 - - + +
111F SER* 1.3 102.8 + - - +
113F ARG* 1.3 65.4 + - - +
114F GLY 3.4 0.2 + - - -
115F HIS* 3.2 44.6 + + + +
138F PRO* 3.5 10.0 - - - +
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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