Contacts of the strand formed by residues 190 - 200 (chain B) in PDB entry 5F0L
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 VAL 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B ASN* 3.9 6.1 + - - +
185B TYR* 3.2 17.7 - - - -
188B LYS 4.7 3.8 - - - +
189B ASP* 1.3 88.5 + - - +
191B ILE* 1.3 64.9 + - - +
192B VAL* 3.3 12.7 + - + +
249B ARG* 3.7 30.3 - - + -
250B LEU 3.5 11.7 - - - +
251B PHE* 3.4 34.3 - - + -
7C ASP* 4.1 2.7 - - - +
9C ARG* 3.7 25.0 + - - +
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Residues in contact with ILE 191 (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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180B TYR* 4.3 17.3 - - + -
185B TYR* 3.4 48.2 - - + +
190B VAL* 1.3 69.0 - - - +
192B VAL* 1.3 59.8 + - - +
209B LEU* 4.3 3.1 - - + -
248B ILE* 3.5 14.1 - - + +
249B ARG* 3.3 6.4 - - - -
250B LEU* 2.9 57.2 + - + +
252B LEU* 4.1 17.9 - - + -
274B LEU* 4.0 29.4 - - + -
292B ILE* 4.1 5.4 - - + -
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Residues in contact with VAL 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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180B TYR* 3.8 0.7 - - - -
181B ASN* 2.9 52.8 + - + +
190B VAL* 3.3 13.8 + - + +
191B ILE* 1.3 74.4 - - - +
193B GLY* 1.3 60.8 + - - +
248B ILE 3.4 5.6 - - - +
249B ARG* 4.7 2.2 - - + -
9C ARG* 3.8 42.2 - - + +
10C ARG* 3.8 31.9 - - - -
11C LEU* 3.8 16.8 - - + +
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Residues in contact with GLY 193 (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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179B GLU 3.0 14.1 - - - -
180B TYR* 4.2 3.1 - - - -
192B VAL* 1.3 76.0 - - - +
194B LYS* 1.3 63.2 + - - +
247B PRO* 3.8 2.4 - - - +
248B ILE* 2.8 45.0 + - - +
10C ARG* 5.8 0.5 - - - -
11C LEU* 3.8 14.3 + - - +
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Residues in contact with LYS 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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165B LYS* 5.0 2.6 - - - +
177B GLU* 3.8 1.4 + - - +
178B PHE* 3.3 3.5 - - - -
179B GLU* 2.8 61.2 + - + +
193B GLY* 1.3 75.7 - - - +
195B ILE* 1.3 70.4 + - - +
196B TYR* 5.0 4.3 - - + +
245B SER* 4.6 4.5 - - - +
246B ILE 3.3 14.8 - - - +
247B PRO* 4.7 2.0 - - + -
248B ILE* 4.1 2.8 - - - +
416B EDO 3.0 42.5 + - - -
11C LEU* 4.0 19.2 - - + +
12C ILE 3.4 24.3 + - - +
13C THR* 4.2 17.0 - - + +
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Residues in contact with ILE 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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176B ILE* 4.4 20.2 - - + -
177B GLU 3.7 2.0 - - - +
178B PHE* 3.4 26.9 - - + -
180B TYR* 4.9 1.6 - - + -
194B LYS* 1.3 76.8 - - - +
196B TYR* 1.3 61.0 + - - +
197B PHE* 3.8 24.1 - - + -
207B MET* 3.8 32.3 - - + -
235B ILE* 3.9 13.5 - - + -
244B GLU 3.7 1.7 - - - +
245B SER* 3.4 3.6 - - - -
246B ILE* 2.8 38.5 + - + +
248B ILE* 3.7 16.2 - - + -
276B LEU* 3.8 15.7 - - + -
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Residues in contact with TYR 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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176B ILE* 3.4 4.8 - - - +
177B GLU* 2.8 51.0 + - + +
194B LYS* 5.0 5.2 - - - -
195B ILE* 1.3 74.3 - - - +
197B PHE* 1.3 62.4 - - - +
198B LEU* 3.4 35.3 + - + +
243B GLY* 3.5 37.4 + - - -
244B GLU 3.5 7.0 - - - -
245B SER* 3.2 22.7 - - - +
416B EDO 3.7 39.3 - - - +
14C LYS* 4.0 28.8 - - + +
15C PRO 5.4 0.5 + - - -
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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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174B LEU* 4.6 0.7 - - + -
175B HIS 4.1 1.1 - - - -
176B ILE* 3.5 21.8 - - + -
195B ILE* 3.8 17.9 - - + -
196B TYR* 1.3 77.5 - - - +
198B LEU* 1.3 61.0 + - - +
200B VAL* 3.6 24.0 - - + -
204B ILE* 4.1 4.3 - - + -
207B MET* 3.9 19.1 - - + -
236B MET* 4.0 4.9 - - + -
240B PRO* 3.6 32.5 - - + -
241B VAL 3.8 16.4 - - - +
242B LYS* 3.5 0.4 - - - -
243B GLY* 2.8 32.3 + - - -
244B GLU* 3.0 21.6 + - + +
246B ILE* 3.8 22.0 - - + -
278B LEU* 3.8 16.8 - - + -
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Residues in contact with LEU 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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167B GLU* 3.9 35.7 - - + +
175B HIS* 3.0 21.1 + - + +
176B ILE* 4.1 15.7 - - - -
177B GLU* 4.2 9.4 - - + -
196B TYR* 3.4 33.2 - - + +
197B PHE* 1.3 74.8 - - - +
199B LEU* 1.3 62.2 + - - +
242B LYS* 3.3 27.9 - - - +
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Residues in contact with LEU 199 (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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172B ASP* 3.9 24.2 - - - +
173B CYS 4.1 8.7 - - - +
174B LEU* 3.3 6.2 - - - +
175B HIS* 3.0 60.8 + - + +
197B PHE 3.7 0.8 - - - -
198B LEU* 1.3 81.8 - - - +
200B VAL* 1.3 67.3 + - - +
201B ARG* 3.7 31.2 - - + +
242B LYS* 4.3 4.4 - - - +
204C GOL 3.6 35.0 - - - +
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Residues in contact with VAL 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B CYS 3.9 1.8 - - - -
174B LEU* 4.2 4.0 - - + -
197B PHE* 3.6 38.8 - - + -
199B LEU* 1.3 81.6 - - - +
201B ARG* 1.3 59.8 + - - +
202B ILE 3.4 21.1 - - - +
204B ILE* 4.1 17.3 - - + +
240B PRO* 3.6 26.5 - - + +
241B VAL* 4.3 12.3 - - - -
242B LYS* 4.4 3.7 - - - +
26C SER* 3.9 21.7 + - - -
27C ASN* 4.1 6.8 + - - +
204C GOL 4.5 2.9 + - - -
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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