Contacts of the helix formed by residues 188 - 202 (chain I) in PDB entry 1F1H
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 ALA 188 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I LEU* 4.6 5.2 - - + -
155I GLU* 4.7 3.6 - - - +
186I ASP* 2.9 6.8 + - - +
187I SER* 1.3 82.8 + - - +
189I GLN* 1.3 64.6 + - - +
190I ASP 3.5 1.8 - - - -
191I ILE* 3.8 23.6 - - + -
192I ARG* 2.9 42.1 + - + +
219I ASN* 3.8 18.2 - - - +
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Residues in contact with GLN 189 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H ASP* 4.1 0.3 - - - +
30H HIS* 2.9 30.3 + - - -
32H THR* 2.9 17.9 + - - +
80H PHE* 3.5 28.6 - - + -
1490H MPD 2.9 50.2 + - + +
183I PRO* 4.3 10.5 - - + -
186I ASP* 4.0 3.6 + - - -
187I SER 3.7 2.4 + - - -
188I ALA* 1.3 76.6 - - - +
190I ASP* 1.3 65.5 + - - +
192I ARG* 2.9 21.8 + - - +
193I SER* 3.1 19.9 + - - -
209I HIS* 3.2 9.6 - - - -
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Residues in contact with ASP 190 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H PHE 4.8 4.7 - - - +
80H PHE* 3.6 1.8 - - - -
81H ALA* 2.7 28.5 + - + +
82H ASP* 4.4 0.2 - - - +
1490H MPD 2.5 43.1 + - - +
187I SER 5.4 0.4 + - - -
189I GLN* 1.3 78.5 - - - +
191I ILE* 1.3 64.8 + - + +
194I GLU* 3.1 26.9 + - - +
249I PHE* 4.4 11.9 - - + -
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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
----------------------------------------------------------
134I LEU* 4.0 10.8 - - + -
187I SER* 3.9 9.4 - - - +
188I ALA* 3.7 30.7 - - + +
189I GLN 3.2 0.4 - - - -
190I ASP* 1.3 76.6 - - + +
192I ARG* 1.3 62.7 + - - +
194I GLU* 3.3 5.7 + - - +
195I MET* 3.1 45.8 + - + +
245I VAL* 4.5 4.7 - - + -
246I ALA* 5.0 3.6 - - - -
249I PHE* 3.7 39.9 - - + -
251I LYS* 4.5 26.5 - - + +
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Residues in contact with ARG 192 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H HIS* 3.7 4.2 + - - -
32H THR* 5.0 0.2 + - - -
132I PHE* 5.4 0.4 - - + -
134I LEU* 5.7 1.6 - - + -
186I ASP* 2.8 39.8 + - - -
188I ALA* 2.9 27.2 + - + +
189I GLN* 2.9 24.9 - - - +
191I ILE* 1.3 76.2 - - + +
193I SER* 1.3 63.6 + - - +
195I MET* 3.0 18.5 + - - +
196I CYS* 2.9 22.9 + - - -
209I HIS* 2.8 37.1 + - + +
210I HIS* 3.4 21.5 - - - +
211I HIS* 3.6 12.8 - - - +
219I ASN* 2.9 43.2 - - + +
220I GLU 4.2 6.1 - - - +
221I VAL* 4.5 5.5 - - + +
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Residues in contact with SER 193 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H PHE* 3.5 14.9 - - - -
82H ASP* 3.5 9.0 - - - -
1490H MPD 2.5 50.4 - - - +
189I GLN 3.1 4.9 + - - -
192I ARG* 1.3 77.9 - - - +
194I GLU* 1.3 63.2 + - - +
196I CYS* 3.1 2.9 + - - +
197I LEU* 2.9 28.0 + - - +
209I HIS* 2.8 20.2 + - - -
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Residues in contact with GLU 194 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82H ASP* 4.5 7.5 + - - +
190I ASP 3.1 12.8 + - - +
191I ILE 3.5 8.7 - - - +
192I ARG 3.2 0.2 - - - -
193I SER* 1.3 75.0 - - - +
195I MET* 1.3 65.1 + - - +
197I LEU* 3.2 20.7 + - - +
198I VAL* 3.0 40.8 + - - +
245I VAL* 4.1 11.8 - - + +
248I ARG* 2.9 30.9 + - - -
249I PHE* 3.7 22.9 - - + -
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Residues in contact with MET 195 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I PHE* 3.8 22.9 - - + -
134I LEU* 4.1 17.7 - - + -
191I ILE* 3.1 32.1 + - + +
192I ARG* 3.0 16.2 + - - +
194I GLU* 1.3 77.4 - - - +
196I CYS* 1.3 56.3 + - - +
198I VAL 3.5 0.2 + - - -
199I MET* 2.9 44.0 + - + +
221I VAL* 4.6 5.4 - - + -
241I VAL* 3.6 13.2 - - + +
242I VAL* 3.7 41.1 - - + +
245I VAL* 3.7 16.2 - - + -
246I ALA 4.2 6.5 - - - +
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Residues in contact with CYS 196 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H PHE* 3.8 16.4 - - + -
192I ARG 2.9 17.0 + - - -
193I SER 3.1 7.4 + - - +
195I MET* 1.3 74.1 - - - +
197I LEU* 1.3 67.2 + - - +
199I MET* 3.2 3.4 + - - +
200I GLU* 3.0 31.2 + - - +
206I VAL* 3.7 34.7 - - + +
209I HIS* 3.7 25.8 - - - -
221I VAL* 3.7 17.0 - - - -
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Residues in contact with LEU 197 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15H LYS* 4.5 22.0 - - + +
16H PHE* 3.4 26.0 - - + -
82H ASP* 3.2 31.4 - - + +
193I SER 2.9 18.1 + - - +
194I GLU* 3.2 17.7 + - - +
196I CYS* 1.3 75.9 - - - +
198I VAL* 1.3 59.1 + - + +
200I GLU* 3.3 10.8 + - - +
201I GLN* 3.0 41.3 + - - +
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Residues in contact with VAL 198 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I PRO* 3.5 34.5 - - + -
79I PHE* 4.2 4.7 - - + -
194I GLU* 3.0 34.1 + - - +
197I LEU* 1.3 73.8 - - + +
199I MET* 1.3 66.7 + - - +
201I GLN* 3.0 19.6 + - - +
202I MET* 3.0 20.4 + - - +
241I VAL* 3.8 25.8 - - + -
245I VAL* 4.4 9.2 - - + -
248I ARG* 4.5 9.2 - - - +
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Residues in contact with MET 199 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195I MET* 2.9 31.7 + - + +
196I CYS 3.6 4.7 - - - +
198I VAL* 1.3 74.7 - - - +
200I GLU* 1.3 58.1 + - - +
202I MET* 2.9 19.6 + - - +
203I GLY 3.4 0.7 + - - -
204I LEU* 3.1 36.6 + - + +
206I VAL* 4.3 4.5 - - + -
221I VAL* 3.7 26.5 - - + -
223I THR* 4.2 7.0 - - - -
237I ILE* 5.9 0.2 - - + -
238I TYR* 3.5 45.3 - - + +
241I VAL* 3.8 20.4 - - + -
242I VAL* 3.6 27.4 - - + -
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Residues in contact with GLU 200 (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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34H PRO* 5.2 2.6 - - - +
36H HIS* 2.7 36.9 + - - -
196I CYS* 3.0 20.9 + - - +
197I LEU* 3.6 10.9 - - - +
199I MET* 1.3 73.5 - - - +
201I GLN* 1.3 60.9 + - - +
202I MET 2.9 5.9 + - - -
203I GLY* 3.0 12.6 + - - -
204I LEU 3.3 18.4 - - - +
205I VAL* 4.0 2.7 - - - +
206I VAL* 3.0 31.4 + - + +
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Residues in contact with GLN 201 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I VAL* 4.0 8.7 - - - +
76I ILE 5.4 0.3 - - - +
78I PRO* 4.3 17.3 - - + +
197I LEU* 3.0 33.9 + - - +
198I VAL* 3.0 19.8 + - - +
200I GLU* 1.3 75.0 - - - +
202I MET* 1.3 62.5 + - + +
203I GLY 3.4 1.5 + - - -
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Residues in contact with MET 202 (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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20I ARG* 5.1 0.7 - - - +
75I VAL* 3.8 28.9 - - + +
76I ILE 4.1 7.4 - - - +
78I PRO* 3.7 28.7 - - + -
86I ILE* 3.6 30.5 - - + -
198I VAL* 3.0 8.8 + - + +
199I MET 2.9 11.5 + - - +
200I GLU 2.9 1.4 - - - -
201I GLN* 1.3 82.2 - - + +
203I GLY* 1.3 57.3 + - - +
204I LEU* 3.5 8.5 + - - +
237I ILE* 3.8 34.3 - - + +
240I TYR* 4.3 12.1 - - + -
241I VAL* 3.6 26.9 - - - -
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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
------------------------------------------------------------
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