Contacts of the strand formed by residues 191 - 198 (chain B) in PDB entry 2AFW
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 191 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B HIS* 3.4 38.8 - - + +
131B ALA* 4.7 1.1 - - - +
133B ARG* 3.3 35.9 - - + +
134B HIS 3.9 2.7 - - - +
135B LEU 3.9 7.4 - - - +
181B LEU* 4.2 13.0 - - - +
189B PRO* 2.8 17.7 + - + +
190B ASP* 1.3 77.1 - - - +
192B SER* 1.3 73.0 + - - +
242B ASP* 4.0 12.1 - - - +
358B TYR* 3.8 19.7 - - + +
359B LEU* 3.9 16.1 - - + +
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Residues in contact with SER 192 (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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127B LEU* 3.2 23.9 + - - +
128B ASN* 2.7 33.7 + - - -
131B ALA* 4.3 2.2 - - - -
133B ARG 3.0 8.1 + - - -
134B HIS* 3.2 10.7 - - - -
135B LEU 2.9 24.4 + - - -
181B LEU* 3.6 10.6 - - - +
191B LEU* 1.3 75.7 - - - +
193B LEU* 1.3 66.1 + - - +
359B LEU* 3.6 15.2 - - - +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B TRP* 3.8 25.3 - - + -
126B THR* 3.8 0.2 - - - -
127B LEU* 2.9 37.5 + - + +
134B HIS* 3.6 4.6 - - - -
135B LEU* 3.6 31.0 - - + +
137B LEU* 4.1 19.7 - - + -
170B LEU* 4.2 17.7 - - + -
178B LEU* 4.0 25.4 - - + -
192B SER* 1.3 83.6 + - - +
194B GLN* 1.3 69.6 + - - +
195B LEU* 4.5 2.5 - - + -
355B VAL* 4.3 10.5 - - + -
359B LEU* 4.1 9.8 - - + +
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Residues in contact with GLN 194 (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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102B TRP* 4.6 0.2 - - - -
124B ILE* 3.6 18.7 - - + +
125B SER 3.4 6.1 - - - +
126B THR* 2.9 31.6 + - + +
134B HIS* 4.1 16.9 + - + +
135B LEU 3.0 11.6 + - - +
136B VAL* 3.3 22.3 - - + +
137B LEU 2.9 24.9 + - - +
193B LEU* 1.3 77.8 - - - +
195B LEU* 1.3 71.8 + - - +
196B ILE* 4.0 15.8 - - + +
223B MET* 4.1 19.0 - - - +
241B MET* 5.2 0.4 - - - +
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Residues in contact with LEU 195 (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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95B ILE* 4.5 6.5 - - + -
102B TRP* 3.7 34.5 - - + -
123B ILE 3.9 0.5 - - - +
124B ILE* 3.5 3.6 - - - +
125B SER* 2.8 41.1 + - - +
137B LEU* 3.2 33.4 - - + -
167B MET* 3.8 33.7 - - + +
168B LEU* 5.7 0.4 - - - -
170B LEU* 5.2 2.2 - - + -
171B ALA* 4.4 7.2 - - + -
193B LEU* 4.5 6.3 - - + -
194B GLN* 1.3 79.4 - - - +
196B ILE* 1.3 64.4 + - - +
197B PHE* 4.0 22.2 - - + -
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Residues in contact with ILE 196 (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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122B ASN* 5.1 1.3 - - + -
123B ILE 3.4 7.6 - - - +
124B ILE* 4.4 9.0 - - + -
136B VAL* 3.6 25.1 - - + -
137B LEU 2.9 7.3 + - - -
138B ALA* 3.1 29.6 - - + +
139B CYS 3.1 6.1 + - - +
167B MET* 3.6 3.2 - - - +
194B GLN* 4.0 17.0 - - + +
195B LEU* 1.3 80.1 - - - +
197B PHE* 1.3 66.3 + - - +
198B PHE* 3.5 40.4 - - + -
219B LEU* 3.8 23.3 - - + -
223B MET* 4.7 8.3 - - - -
241B MET* 4.7 7.0 - - + -
244B LEU* 5.0 0.9 - - + -
310B PHE* 5.1 1.3 - - + -
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Residues in contact with PHE 197 (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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91B ILE* 3.6 44.9 - - + -
95B ILE* 4.0 13.5 - - + -
122B ASN* 3.7 0.9 - - - -
123B ILE* 2.8 49.8 + - + -
125B SER* 4.8 1.1 - - - -
139B CYS* 3.4 21.3 - - - -
141B TYR* 3.5 20.5 - - + -
164B CYS* 3.9 25.4 - - - -
167B MET* 3.8 22.7 - - + -
168B LEU* 4.1 13.9 - - + -
195B LEU* 4.0 19.7 - - + -
196B ILE* 1.3 75.6 - - - +
198B PHE* 1.3 64.5 + - - +
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Residues in contact with PHE 198 (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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122B ASN* 3.4 9.9 - - - +
138B ALA* 3.8 20.4 - - + -
139B CYS 2.8 25.1 + - - +
140B HIS* 3.3 4.5 - - + +
141B TYR* 2.8 30.7 + - - -
142B ASP* 3.7 0.2 - - - +
196B ILE* 3.5 27.8 - - + -
197B PHE* 1.3 73.2 - - - +
199B ASP* 1.3 67.0 + - - +
215B GLY 4.0 0.9 - - - -
216B SER* 3.6 29.6 - - - +
219B LEU* 3.8 12.6 - - + -
244B LEU* 5.2 5.2 - - + -
246B LEU* 4.5 3.4 - - + -
306B ASP* 3.5 45.3 - - + +
310B PHE* 3.5 26.2 - + - -
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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