Contacts of the strand formed by residues 106 - 111 (chain B) in PDB entry 6B0Z
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 THR 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLY* 1.3 72.0 - - - -
107B VAL* 1.3 66.9 + - - +
108B PHE* 3.7 30.4 - - + -
132B HIS 3.4 15.0 - - - +
133B HIS* 3.3 18.0 + - - +
191B ASP 4.1 0.5 + - - -
192B PHE* 3.6 38.9 + - + -
195B SER* 3.9 12.5 + - - -
294B VAL 3.6 0.9 - - - +
295B LEU* 3.5 5.1 - - - +
296B VAL* 2.8 30.4 + - - -
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ARG* 4.6 9.9 - - + -
106B THR* 1.3 70.6 - - - +
108B PHE* 1.3 65.9 + - - +
109B ARG* 3.9 9.6 - - + +
130B ILE 3.6 1.2 - - - +
131B GLY* 3.4 3.5 - - - -
132B HIS* 2.9 65.8 + - + +
134B ALA* 4.1 14.8 - - + -
293B SER* 3.7 22.4 - - - +
294B VAL 3.4 5.4 - - - +
295B LEU* 3.9 22.0 - - + -
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Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B THR* 3.7 30.7 - - + -
107B VAL* 1.3 73.2 - - - +
109B ARG* 1.3 62.3 + - - +
110B GLU* 5.7 0.2 - - - -
129B ILE* 3.6 24.7 - - + -
130B ILE 3.3 3.1 - - - -
131B GLY* 3.6 22.4 - - - -
195B SER* 3.7 29.6 - - - -
196B SER* 3.9 12.3 - - - -
199B MET* 3.7 31.9 - - + -
266B ILE* 4.4 8.3 - - + -
292B THR* 5.4 0.9 - - - +
293B SER* 3.4 4.5 - - - -
294B VAL* 2.8 47.0 + - + +
296B VAL* 3.8 23.8 - - + -
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Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B VAL* 3.9 9.1 - - + +
108B PHE* 1.3 75.5 - - - +
110B GLU* 1.3 62.4 + - - +
129B ILE* 3.2 8.0 - - - +
130B ILE* 2.9 35.2 + - + +
132B HIS* 2.8 40.0 + - - +
272B TYR* 4.7 2.7 - - - -
274B GLY* 3.5 16.8 + - - -
275B ASP* 3.5 14.3 + - - -
278B SER* 3.5 20.6 - - - +
279B ASP* 2.5 41.3 + - - +
291B MET* 4.6 3.8 - - + -
292B THR 3.4 11.7 - - - +
293B SER* 4.5 9.8 - - - -
308B ALA* 4.7 5.5 + - - +
502B C81 3.5 15.3 - - + +
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B ARG* 1.3 77.3 - - - +
111B ALA* 1.3 72.8 + - - +
112B ILE* 6.1 0.7 - - + -
127B PRO* 3.4 26.5 - - + +
128B ILE 3.7 6.3 - - - +
129B ILE* 3.7 30.8 - - + +
203B LYS* 4.3 12.7 + - - -
205B TRP* 4.4 2.8 - - - -
291B MET* 3.9 4.7 - - - -
292B THR* 2.9 47.3 + - + +
338B ARG* 3.3 33.5 + - - -
502B C81 3.8 1.3 - - - +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLU* 1.3 88.9 - - - +
112B ILE* 1.3 61.5 + - - +
113B ILE* 4.4 5.6 - - + -
127B PRO* 3.5 15.8 - - - +
287B SER* 6.3 2.0 - - - -
290B MET* 3.6 7.2 - - + +
291B MET* 3.9 15.6 - - + -
502B C81 3.4 51.0 + - + +
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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