Contacts of the strand formed by residues 133 - 140 (chain B) in PDB entry 2AFU
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 ARG 133 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B TRP* 4.0 22.2 - - + +
39B GLU* 2.8 56.0 + - - +
40B LYS 4.1 5.0 - - - +
43B HIS* 3.4 35.4 - - - +
131B ALA 2.7 6.3 + - - +
132B LYS* 1.3 81.4 - - + +
134B HIS* 1.3 67.9 + - - +
190B ASP* 3.3 17.9 + - - +
191B LEU* 3.3 20.5 - - + +
192B SER 2.8 22.5 + - - -
239B HIS 5.8 0.2 - - - +
240B GLY* 3.4 5.4 - - - +
242B ASP* 2.8 42.2 + - - +
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Residues in contact with HIS 134 (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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126B THR* 3.4 14.7 - - + +
127B LEU 2.7 30.0 + - - -
128B ASN 2.9 15.6 + - - -
129B PRO 4.0 7.2 - - - -
131B ALA* 2.7 33.7 + - + +
132B LYS 4.7 1.2 + - - -
133B ARG* 1.3 72.4 - - - +
135B LEU* 1.3 66.6 + - - +
136B VAL* 3.7 5.9 + - + +
191B LEU* 3.9 5.8 - - - +
192B SER* 3.2 24.2 - - - -
193B LEU 3.5 10.8 - - - -
194B GLN* 4.2 15.1 + - + +
228B HIS* 4.9 3.7 + - - -
240B GLY 3.0 10.9 + - - +
241B MET* 3.7 3.7 - - - -
242B ASP* 3.0 23.8 + - - -
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Residues in contact with LEU 135 (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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134B HIS* 1.3 72.9 - - - +
136B VAL* 1.3 63.0 + - - +
137B LEU* 4.5 6.5 - - + -
191B LEU* 4.0 1.4 - - - +
192B SER 2.8 12.6 + - - +
193B LEU* 3.3 21.1 - - + +
194B GLN 3.0 23.6 + - - -
242B ASP* 4.6 4.5 - - - -
243B LEU* 3.9 28.5 - - + +
245B VAL* 4.2 15.3 - - + -
354B PHE* 4.6 4.3 - - + -
355B VAL* 4.2 26.5 - - + +
358B TYR* 3.8 48.0 - - + -
359B LEU* 4.4 5.2 - - + -
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Residues in contact with VAL 136 (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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134B HIS* 3.9 13.0 - - + +
135B LEU* 1.3 78.9 - - - +
137B LEU* 1.3 66.3 + - - +
194B GLN* 3.4 27.8 - - + +
196B ILE* 3.6 30.5 - - + -
241B MET* 3.8 27.4 - - + -
243B LEU 2.9 16.1 + - - +
244B LEU* 3.8 15.9 - - + -
245B VAL* 2.7 35.7 + - - +
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Residues in contact with LEU 137 (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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135B LEU* 4.5 7.2 - - + -
136B VAL* 1.3 77.0 - - - +
138B ALA* 1.3 62.3 + - - +
167B MET* 3.4 15.4 - - + +
170B LEU* 3.9 25.8 - - + -
193B LEU* 4.3 12.6 - - + -
194B GLN 3.0 6.1 + - - -
195B LEU* 3.3 19.3 - - + -
196B ILE 2.9 24.1 + - - -
245B VAL* 3.4 35.0 - - + +
247B LEU* 5.2 2.7 - - + -
351B LEU* 4.4 13.5 - - + -
354B PHE* 5.8 0.7 - - + -
355B VAL* 3.7 32.1 - - + -
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Residues in contact with ALA 138 (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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136B VAL* 4.7 0.2 - - + -
137B LEU* 1.3 76.4 - - - +
139B CYS* 1.3 63.6 + - - +
167B MET* 3.6 6.8 - - - +
196B ILE* 3.1 26.7 - - + +
198B PHE* 3.9 18.4 - - + -
244B LEU* 4.1 16.6 - - + -
245B VAL 2.9 7.9 + - - +
246B LEU* 3.5 6.9 - - + +
247B LEU* 2.9 30.3 + - - +
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Residues in contact with CYS 139 (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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138B ALA* 1.3 78.0 - - - +
140B HIS* 1.3 61.6 + - - +
160B SER* 4.6 0.7 - - - -
163B PRO* 3.7 14.1 - - + -
164B CYS* 3.4 42.0 - - - -
167B MET* 3.5 19.5 - - - -
196B ILE 3.2 5.5 + - - +
197B PHE* 3.4 8.7 - - - -
198B PHE* 2.8 28.6 + - - -
246B LEU* 3.8 6.0 - - - +
247B LEU* 3.4 20.4 - - + +
306B ASP* 4.5 1.1 - - - -
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Residues in contact with HIS 140 (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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139B CYS* 1.3 77.7 - - - +
141B TYR* 1.3 60.1 + - - +
142B ASP* 2.7 39.9 + - - +
159B ASP* 2.7 36.2 + - - -
160B SER* 3.2 39.2 + - - +
164B CYS* 3.8 6.2 - - - -
198B PHE* 3.1 12.6 - - + +
201B GLN* 3.3 45.2 + - + +
202B GLU* 4.0 9.0 - - + -
246B LEU* 5.2 0.2 - - - +
248B ASP* 3.7 8.1 - - + -
306B ASP* 3.4 10.7 + - - +
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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