Contacts of the strand formed by residues 184 - 191 (chain I) in PDB entry 1XFB
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 184 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16I LEU* 3.2 40.4 - - + +
19I ILE* 3.6 21.5 - - + -
20I ALA* 3.9 11.9 - - + +
23I ILE* 5.2 0.2 - - + -
144I ASP 2.8 14.0 + - - +
145I PHE* 2.9 16.0 - - + +
146I ALA 2.8 26.5 + - - -
183I ILE* 1.3 69.9 - - - +
185I PRO* 1.3 67.9 - - - +
186I ILE* 5.8 0.4 - - + -
226I GLY 3.3 22.7 - - - +
227I THR* 3.9 11.9 - - - +
228I LEU* 4.6 8.5 - - + +
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Residues in contact with PRO 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146I ALA 3.9 1.6 - - - +
174I TYR* 3.5 23.8 - - + +
175I ALA* 3.8 36.3 - - + +
178I CYS* 3.8 9.2 - - + -
179I GLN* 3.8 9.2 - - + -
183I ILE 3.2 7.6 - - - +
184I VAL* 1.3 86.4 - - - +
186I ILE* 1.3 61.4 + - - +
187I VAL* 3.6 3.3 + - + +
226I GLY 3.2 16.6 - - - +
227I THR* 3.6 13.1 - - + -
228I LEU 3.2 21.5 + - - +
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Residues in contact with ILE 186 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ILE* 3.8 20.4 - - + -
78I ILE* 4.1 14.6 - - + -
145I PHE* 3.6 36.3 - - + -
146I ALA 2.8 18.9 + - - +
147I LYS* 4.3 5.4 - - + -
148I TRP 3.7 7.3 + - - -
174I TYR* 2.9 18.4 + - - -
184I VAL 5.1 0.7 - - - +
185I PRO* 1.3 71.9 - - - +
187I VAL* 1.3 61.4 + - - +
188I GLU* 3.4 4.7 + - + +
228I LEU* 3.4 24.5 - - + +
230I LYS* 3.4 39.0 - - + +
269I THR* 4.5 4.9 - - - +
301I SER* 4.9 1.1 - - - +
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Residues in contact with VAL 187 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I LEU* 3.5 37.9 - - + -
174I TYR* 4.4 8.1 - - + -
175I ALA* 4.5 20.0 - - + -
185I PRO 4.3 7.0 - - - +
186I ILE* 1.3 70.6 - - - +
188I GLU* 1.3 56.8 + - - +
189I PRO* 3.1 10.1 - - + +
213I VAL* 3.9 18.4 - - + -
214I TYR* 5.7 0.9 - - - +
217I LEU* 4.4 19.1 - - + -
227I THR* 4.8 7.4 - - - -
228I LEU 2.8 17.2 + - - +
229I LEU* 3.4 8.6 - - + +
230I LYS 3.0 20.8 + - - -
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Residues in contact with GLU 188 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I LYS* 2.8 36.3 + - + +
148I TRP 3.3 14.6 + - - +
149I ARG* 3.3 31.0 - - + +
150I CYS* 3.0 24.1 + - - +
171I LEU* 4.0 5.1 - - - +
186I ILE* 3.4 6.5 + - + +
187I VAL* 1.3 73.9 - - - +
189I PRO* 1.3 58.5 - - - +
190I GLU* 3.3 14.6 + - + +
230I LYS* 3.3 41.0 - - + +
271I LEU* 3.7 11.5 - - + +
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Residues in contact with PRO 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150I CYS* 4.2 7.4 - - + +
152I LEU* 5.6 4.7 - - + -
171I LEU* 3.8 17.5 - - + -
187I VAL* 3.1 17.3 - - + +
188I GLU* 1.3 82.4 - - - +
190I GLU* 1.3 62.3 + - - +
191I ILE* 3.4 9.0 + - - +
209I VAL* 4.2 11.1 - - + +
210I LEU* 4.0 26.7 - - + -
213I VAL* 4.1 14.8 - - + -
229I LEU* 3.8 10.1 - - + -
230I LYS 3.8 7.4 - - - +
231I PRO* 4.5 6.1 - - + +
232I ASN* 3.6 8.3 + - - -
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Residues in contact with GLU 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149I ARG* 2.4 30.6 + - - +
150I CYS 3.2 16.0 + - - +
151I VAL* 3.4 3.1 - - - +
152I LEU* 2.8 27.3 + - - +
188I GLU* 3.3 17.7 + - - +
189I PRO* 1.3 71.4 - - - +
191I ILE* 1.3 67.7 + - - +
192I LEU* 3.2 23.6 + - + +
193I PRO* 4.7 4.5 - - - +
232I ASN* 4.0 3.6 - - + +
271I LEU* 3.7 39.8 - - + +
273I GLY* 5.0 6.0 - - - -
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Residues in contact with ILE 191 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152I LEU* 3.6 22.2 - - + +
154I ILE* 3.5 37.7 - - + -
189I PRO 4.2 5.4 - - - +
190I GLU* 1.3 74.9 - - - +
192I LEU* 1.3 65.2 + - - +
193I PRO* 3.7 3.3 - - - +
202I CYS* 5.2 5.0 - - - -
205I VAL* 3.7 4.5 - - + -
206I THR* 3.4 41.7 - - + +
209I VAL* 3.6 26.0 - - + -
232I ASN* 2.7 39.0 - - - +
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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