Contacts of the helix formed by residues 187 - 200 (chain C) in PDB entry 5FI0
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 PRO 187 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C MET* 4.6 3.6 - - + -
182C LYS 6.1 0.2 - - - +
185C ASP 3.3 9.2 - - - +
186C ILE* 1.3 97.6 - - + +
188C LEU* 1.3 68.4 + - - +
189C GLU* 3.1 22.0 - - + +
190C GLY 3.0 13.0 + - - -
191C TYR* 3.6 8.4 - - - -
2D GLN* 5.4 10.5 - - - +
3D ALA* 5.1 6.1 - - + -
56D TRP* 4.6 14.4 - - + +
74D GLN* 6.1 0.4 - - - +
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Residues in contact with LEU 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C LEU* 3.8 17.3 - - + -
75C PHE* 3.7 37.9 - - + -
99C LEU* 4.4 8.3 - - + -
100C PHE* 4.4 2.2 - - + -
159C LEU* 4.2 21.5 - - + -
172C LEU* 4.3 13.5 - - + -
176C MET* 3.5 22.5 - - + +
187C PRO* 1.3 74.4 - - - +
189C GLU* 1.3 60.5 + - - +
191C TYR* 3.1 6.1 + - + -
192C LEU* 2.9 56.4 + - + +
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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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152C HIS* 4.6 3.7 + - - -
156C LEU* 5.3 10.5 - - + -
159C LEU* 3.5 30.8 - - + +
160C VAL* 5.5 3.9 - - + +
163C ASN* 3.9 17.1 + - - -
187C PRO* 3.1 25.2 + - + +
188C LEU* 1.3 75.8 + - - +
190C GLY* 1.3 56.4 + - - +
192C LEU* 3.6 5.8 + - - +
193C LEU* 3.0 27.7 + - - +
5D LYS* 5.8 2.7 - - - +
56D TRP* 4.1 10.7 - - + -
74D GLN* 3.5 26.6 + - - +
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Residues in contact with GLY 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C ILE* 3.9 4.9 - - - -
187C PRO 3.0 10.5 + - - -
189C GLU* 1.3 74.8 - - - +
191C TYR* 1.3 62.1 + - - +
193C LEU* 3.0 3.3 + - - +
194C SER* 2.9 24.8 + - - -
39D ASN* 3.4 20.6 + - - -
56D TRP* 3.4 26.4 - - - -
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Residues in contact with TYR 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C THR* 3.6 28.3 - - + -
70C PHE* 3.8 24.9 - + - -
71C LEU* 3.6 28.1 - - + +
176C MET* 4.5 7.6 - - - -
181C ARG* 2.9 44.5 + - + +
185C ASP* 5.8 2.3 - - - +
186C ILE* 3.4 30.7 + - + +
187C PRO 3.6 14.4 - - - -
188C LEU* 3.1 8.7 + - + +
190C GLY* 1.3 74.3 - - - +
192C LEU* 1.3 63.5 + - - +
194C SER* 2.6 28.1 + - - -
195C PRO* 3.7 1.4 - - - +
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Residues in contact with LEU 192 (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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71C LEU* 4.5 9.6 - - + -
99C LEU* 4.1 33.4 - - + +
100C PHE* 3.5 33.7 - - + -
103C ILE* 4.9 1.1 - - + -
148C TYR* 2.6 35.2 + - - +
152C HIS* 3.4 17.5 + - + +
155C ALA* 5.7 3.6 - - + -
156C LEU* 6.2 1.3 - - - -
159C LEU* 4.2 13.2 - - + -
188C LEU* 2.9 41.6 + - + +
189C GLU* 4.0 5.6 - - - +
191C TYR* 1.3 76.9 - - - +
193C LEU* 1.3 60.9 + - - +
195C PRO* 3.3 3.8 - - - +
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Residues in contact with LEU 193 (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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152C HIS* 3.6 26.9 - - + +
189C GLU 3.0 19.3 + - - +
190C GLY* 3.0 6.0 + - - +
192C LEU* 1.3 80.9 - - - +
194C SER* 1.3 64.3 + - - +
195C PRO 3.0 2.3 - - - -
196C ILE* 3.0 35.1 + - + +
197C GLN* 3.4 30.0 + - + +
56D TRP* 3.5 28.7 - - + -
70D LEU* 4.0 14.8 - - + +
71D SER* 3.7 22.4 - - - +
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Residues in contact with SER 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C TYR* 4.2 10.6 - - - -
67C THR* 3.7 20.7 - - - +
68C LEU* 5.2 0.7 - - - +
71C LEU* 4.9 0.9 - - - +
190C GLY 2.9 11.8 + - - -
191C TYR* 2.6 23.6 + - - -
193C LEU* 1.3 74.9 - - - +
195C PRO* 1.4 63.9 - - - +
197C GLN* 3.7 13.6 - - - +
198C ARG* 2.9 30.0 + - - +
39D ASN* 5.3 2.0 - - - -
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Residues in contact with PRO 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C TYR* 3.3 24.5 - - - +
68C LEU* 4.5 4.9 - - + -
103C ILE* 4.2 14.1 - - + -
106C ILE* 4.3 7.2 - - + -
145C TYR* 3.5 19.2 - - + -
148C TYR* 3.7 29.8 - - + +
191C TYR 3.7 2.9 - - - +
192C LEU 3.3 15.3 - - - +
193C LEU 3.3 1.6 - - - +
194C SER* 1.4 98.3 - - - +
196C ILE* 1.3 62.8 + - - +
198C ARG 3.1 0.9 + - - -
199C ILE* 2.9 22.0 + - - +
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Residues in contact with ILE 196 (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 TYR* 4.5 8.3 - - + -
149C CYS* 3.7 25.5 - - - -
152C HIS* 3.2 39.0 - - + +
193C LEU* 3.0 21.7 + - + +
195C PRO* 1.3 77.3 - - - +
197C GLN* 1.3 64.7 + - + +
199C ILE* 3.3 21.5 - - - +
200C CYS* 3.6 9.9 - - - -
61D GLN* 4.8 9.2 - - - +
67D LEU* 4.5 32.5 - - + +
70D LEU* 3.6 20.2 - - + -
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Residues in contact with GLN 197 (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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193C LEU* 3.4 41.2 + - + +
194C SER* 3.7 11.4 - - - +
196C ILE* 1.3 76.6 - - + +
198C ARG* 1.3 61.2 + - - +
200C CYS* 3.4 10.7 + - - +
201C LYS* 3.2 29.2 + - - +
39D ASN* 3.0 37.4 + - - +
56D TRP* 4.7 4.0 - - - +
57D ASP 3.1 26.5 + - - +
59D ALA 5.0 0.3 - - - +
61D GLN* 4.1 21.5 + - - +
71D SER* 4.3 4.2 + - - +
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Residues in contact with ARG 198 (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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57C ILE* 3.9 2.4 + - - +
60C THR* 3.1 45.1 + - - -
61C GLU* 3.0 32.9 + - - +
64C TYR* 3.5 38.0 - - + +
145C TYR* 4.7 0.2 - - - +
194C SER 2.9 19.7 + - - +
195C PRO 3.6 2.7 - - - +
197C GLN* 1.3 73.8 - - - +
199C ILE* 1.3 63.5 + - - +
200C CYS 3.1 1.6 - - - -
201C LYS* 2.9 32.5 + - - +
202C TYR* 2.9 44.9 + - + +
205C LEU* 4.3 7.0 - - - +
36D VAL* 4.0 19.1 - - - +
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Residues in contact with ILE 199 (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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142C PHE* 4.4 7.4 - - + -
145C TYR* 3.4 42.4 - - + -
149C CYS* 5.1 3.1 - - - -
195C PRO 2.9 10.4 + - - +
196C ILE* 3.3 18.8 - - - +
198C ARG* 1.3 77.0 - - - +
200C CYS* 1.3 70.6 + - - +
202C TYR* 3.6 26.9 - - + +
203C PRO* 3.4 9.7 - - - +
230C MET* 4.1 14.2 - - + +
233C VAL* 4.3 11.9 - - + -
234C CYS* 3.2 18.3 - - - -
237C ILE* 3.9 21.8 - - + -
67D LEU* 5.3 2.5 - - + -
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Residues in contact with CYS 200 (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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196C ILE 3.6 13.7 - - - +
197C GLN 3.4 9.8 + - - +
198C ARG 3.1 0.8 - - - -
199C ILE* 1.3 83.0 - - - +
201C LYS* 1.3 63.4 + - - +
203C PRO* 3.4 11.3 - - - +
204C LEU* 4.3 3.8 - - - +
234C CYS* 3.9 8.7 - - - -
59D ALA 4.9 0.9 - - - +
60D GLY* 3.6 33.8 - - - +
61D GLN* 3.9 18.8 - - + -
64D TYR* 3.8 25.6 - - - -
67D LEU* 4.1 19.1 - - - -
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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