Contacts of the strand formed by residues 183 - 190 (chain C) in PDB entry 1FBA
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 183 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.4 39.3 - - + +
18C ILE* 3.7 22.4 - - + -
19C ALA* 4.1 13.7 - - + +
22C ILE* 4.8 0.9 - - + -
143C ASP 3.0 13.6 + - - +
144C PHE* 3.1 13.7 - - + +
145C ALA 2.8 26.3 + - - -
182C ILE* 1.3 70.8 - - - +
184C PRO* 1.3 74.3 - - - +
185C ILE* 3.7 0.4 + - + -
225C GLY 3.7 13.5 - - - +
226C THR* 4.3 5.6 - - - -
227C LEU* 4.5 12.6 - - + -
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Residues in contact with PRO 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145C ALA 4.0 0.2 - - - +
173C TYR* 3.6 20.9 - - + +
174C ALA* 3.7 43.3 - - + +
177C CYS* 3.9 8.5 - - + -
178C GLN* 3.8 10.5 - - + -
182C ILE 3.2 11.4 - - - +
183C VAL* 1.3 83.6 - - - +
185C ILE* 1.3 62.3 + - - +
186C VAL* 3.8 2.0 + - + +
225C GLY 3.4 13.5 - - - +
226C THR* 3.6 13.2 - - + -
227C LEU 3.3 21.8 + - - +
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Residues in contact with ILE 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 3.6 21.5 - - + -
77C ILE* 4.7 9.0 - - + -
144C PHE* 3.5 35.2 - - + -
145C ALA 3.0 19.1 + - - +
146C LYS* 4.8 4.5 - - + -
147C TRP 4.0 8.1 + - - +
173C TYR* 2.9 18.9 + - - -
183C VAL* 4.8 1.3 - - + +
184C PRO* 1.3 72.7 - - - +
186C VAL* 1.3 63.5 - - - +
187C GLU* 3.6 5.1 + - + +
227C LEU* 3.5 25.8 - - + +
228C LEU 4.5 0.7 - - - -
229C LYS* 3.4 40.2 - - + +
268C THR* 4.2 6.3 - - - +
300C SER* 5.2 1.3 - - - +
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Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C LEU* 4.3 24.2 - - + +
173C TYR* 4.6 4.0 - - + -
174C ALA* 4.4 22.0 - - + -
184C PRO 4.3 6.5 - - - +
185C ILE* 1.3 72.2 - - - +
187C GLU* 1.3 56.9 + - - +
188C PRO* 3.2 7.3 - - + +
212C VAL* 3.9 28.3 - - + -
213C TYR* 5.2 1.8 - - - +
216C LEU* 4.5 18.4 - - + -
226C THR* 4.7 6.5 - - - +
227C LEU 2.9 19.3 + - - +
228C LEU* 3.3 12.1 - - + +
229C LYS 2.7 28.9 + - - -
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Residues in contact with GLU 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LYS* 3.5 28.2 + - + +
147C TRP 3.2 18.6 + - - +
148C ARG* 3.4 27.3 - - + +
149C CYS* 2.9 28.1 + - - +
170C LEU* 3.9 6.3 - - - +
185C ILE* 3.6 4.2 + - + +
186C VAL* 1.3 72.0 - - - +
188C PRO* 1.3 59.8 - - - +
189C GLU* 4.1 6.2 - - - +
229C LYS* 3.3 45.9 + - + +
270C LEU* 3.8 18.0 - - + +
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Residues in contact with PRO 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C CYS* 4.0 6.1 - - + +
151C LEU* 4.8 7.2 - - + -
166C ASN* 6.5 0.2 - - + -
170C LEU* 3.8 18.4 - - + -
186C VAL* 3.2 14.6 - - + +
187C GLU* 1.3 83.4 - - - +
189C GLU* 1.3 62.5 + - - +
190C VAL* 3.5 4.5 + - - +
208C VAL* 4.1 20.2 - - + +
209C LEU* 4.1 16.7 - - + +
212C VAL* 4.1 12.3 - - + -
228C LEU* 3.8 17.0 - - + -
229C LYS 3.5 8.7 - - - +
230C PRO* 4.4 5.9 - - + +
231C ASN* 3.5 12.1 - - - +
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Residues in contact with GLU 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C ARG* 3.0 38.7 + - - +
149C CYS 2.9 18.4 + - - +
150C VAL* 3.4 3.3 - - + +
151C LEU* 2.8 31.6 + - - +
187C GLU* 3.5 10.6 + - - +
188C PRO* 1.3 72.0 - - - +
190C VAL* 1.3 66.9 + - - +
191C LEU* 3.6 12.8 + - + +
192C PRO* 4.3 11.3 - - - +
231C ASN* 4.1 2.2 - - - -
270C LEU* 3.8 38.4 - - + +
272C GLY* 4.3 8.0 - - - -
361C HIS* 4.5 4.0 - - - -
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Residues in contact with VAL 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C LEU* 3.5 15.7 - - + +
153C ILE* 3.6 38.4 - - + -
188C PRO 4.4 3.4 - - - +
189C GLU* 1.3 74.3 - - - +
191C LEU* 1.3 64.9 + - - +
192C PRO* 3.7 2.6 - - - +
201C ALA* 6.0 0.9 - - + -
204C VAL* 3.9 9.6 - - + -
205C THR* 4.3 13.5 - - + +
208C VAL* 4.2 28.9 - - + -
231C ASN* 3.1 41.2 + - - +
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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