Contacts of the strand formed by residues 106 - 112 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75L ILE* 5.4 2.5 - - - -
76L PHE 3.1 12.6 - - - -
77L CYS* 4.0 15.2 - - - -
101L LEU* 4.1 3.6 - - - -
105L THR* 1.3 77.4 - - - +
107L ARG* 1.3 63.3 + - - +
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Residues in contact with ARG 107 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ILE* 3.5 7.2 - - - +
76L PHE* 2.8 39.1 + - + +
86L PRO* 5.5 1.0 - - - +
99L PRO* 3.0 45.8 + - - +
100L THR 3.1 21.0 + - - -
101L LEU* 3.7 23.6 - - + +
102L PRO* 4.5 5.9 - - - +
106L GLY* 1.3 76.0 - - - +
108L ARG* 1.3 60.3 + - - +
109L ILE* 3.5 27.6 + - + +
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Residues in contact with ARG 108 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L GLN* 2.9 47.2 - - + +
74L VAL 3.5 10.8 - - - +
75L ILE* 4.4 9.9 - - + +
107L ARG* 1.3 74.8 - - - +
109L ILE* 1.3 70.7 + - - +
110L HIS* 3.7 21.2 + - + -
146L PRO* 5.7 6.3 - - + -
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Residues in contact with ILE 109 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L GLN* 3.7 6.0 - - - +
74L VAL* 2.6 42.8 + - + +
76L PHE* 3.5 48.5 - - + -
98L TYR* 5.9 7.6 - - + -
107L ARG* 3.5 29.6 - - + +
108L ARG* 1.3 85.9 - - - +
110L HIS* 1.3 78.1 + - - +
111L SER* 4.4 4.3 - - - +
117L TRP* 4.4 15.7 - - + -
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Residues in contact with HIS 110 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72L SER 4.2 2.2 - - - -
73L GLN* 3.5 32.8 + - + +
98L TYR* 6.2 0.2 - - - -
108L ARG* 3.7 19.3 + - - -
109L ILE* 1.3 82.5 - - - +
111L SER* 1.3 61.4 + - - +
112L TYR* 4.8 9.0 - - + +
117L TRP* 5.4 1.6 - - - -
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Residues in contact with SER 111 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71L PRO* 3.6 3.6 - - - +
72L SER 2.9 30.9 + - - -
74L VAL* 4.2 7.4 - - - -
109L ILE* 3.8 6.2 + - - -
110L HIS* 1.3 76.9 - - - +
112L TYR* 1.3 87.2 + - - -
115L HIS* 3.7 10.0 + - - +
117L TRP* 3.2 29.7 + - - -
138L PRO* 3.4 17.7 - - - +
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Residues in contact with TYR 112 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68L SER 3.7 12.8 - - - +
69L ARG* 3.7 18.4 - - + -
70L GLU 3.1 28.9 - - - +
71L PRO* 3.6 19.1 - - + -
72L SER* 3.7 8.3 + - - +
110L HIS* 4.8 7.9 - - + +
111L SER* 1.3 103.9 + - - +
113L ARG* 1.3 66.0 + - - +
114L GLY 3.3 0.2 + - - -
115L HIS* 3.3 43.5 + + + +
138L PRO* 3.4 10.2 - - - +
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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