Contacts of the helix formed by residues 188 - 202 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134K LEU* 4.5 4.7 - - + -
155K GLU* 4.7 3.4 - - - +
186K ASP* 2.9 6.8 + - - +
187K SER* 1.3 82.5 - - - +
189K GLN* 1.3 63.6 + - - +
190K ASP 3.5 1.8 - - - -
191K ILE* 3.8 23.8 - - + -
192K ARG* 2.9 42.9 + - + +
219K ASN* 3.8 18.6 - - - +
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Residues in contact with GLN 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18J ASP* 4.8 0.2 - - - -
30J HIS* 2.9 19.8 + - - -
32J THR* 3.0 19.5 + - - +
80J PHE* 3.5 28.0 - - + -
1492J MPD 2.8 51.2 + - + +
183K PRO* 4.3 9.9 - - + -
186K ASP* 4.0 3.4 + - - -
187K SER 3.7 2.8 - - - -
188K ALA* 1.3 76.1 - - - +
190K ASP* 1.3 63.1 + - - +
192K ARG* 2.9 30.1 - - - +
193K SER* 3.1 20.4 + - - -
209K HIS* 3.2 9.8 - - - -
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Residues in contact with ASP 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J PHE 4.9 4.3 - - - +
80J PHE* 3.6 2.1 - - - -
81J ALA* 2.7 28.8 + - + +
82J ASP* 4.4 0.2 - - - +
1492J MPD 2.6 42.9 + - - +
187K SER 5.4 0.4 + - - -
188K ALA 3.5 0.2 - - - -
189K GLN* 1.3 78.1 - - - +
191K ILE* 1.3 64.5 + - + +
194K GLU* 3.1 26.3 + - - +
249K PHE* 4.4 12.1 - - + -
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Residues in contact with ILE 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K LEU* 4.0 10.1 - - + -
187K SER* 3.9 10.1 - - - +
188K ALA* 3.7 30.3 - - + +
189K GLN 3.2 0.4 - - - -
190K ASP* 1.3 75.7 - - + +
192K ARG* 1.3 62.6 + - - +
194K GLU* 3.3 4.7 + - - +
195K MET* 3.1 46.3 + - + +
245K VAL* 4.5 4.9 - - + -
246K ALA* 5.0 3.8 - - - -
249K PHE* 3.7 40.8 - - + -
251K LYS* 4.5 26.2 - - + +
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Residues in contact with ARG 192 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30J HIS* 3.7 4.6 + - - -
132K PHE* 5.4 0.4 - - + -
134K LEU* 5.7 1.6 - - + -
186K ASP* 2.8 40.6 + - - -
188K ALA* 2.9 25.7 + - + +
189K GLN* 2.9 24.7 - - - +
191K ILE* 1.3 76.3 - - + +
193K SER* 1.3 58.0 + - - +
195K MET* 3.0 19.0 + - - +
196K CYS* 2.9 28.4 + - - -
209K HIS* 2.8 37.3 + - + +
210K HIS* 3.4 20.4 - - - +
211K HIS 3.6 13.0 - - - +
219K ASN* 2.9 43.5 - - + +
220K GLU 4.2 5.6 - - - -
221K VAL* 4.5 5.3 - - + +
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Residues in contact with SER 193 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J PHE* 3.5 15.6 - - - -
82J ASP* 3.5 9.6 - - - -
1492J MPD 2.5 50.2 - - - +
189K GLN 3.1 5.1 + - - -
192K ARG* 1.3 76.0 - - - +
194K GLU* 1.3 63.5 + - - +
196K CYS* 3.1 2.5 + - - +
197K LEU* 2.9 28.5 + - - +
209K HIS* 2.8 18.9 + - - -
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Residues in contact with GLU 194 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82J ASP* 4.5 7.7 + - - +
190K ASP 3.1 13.0 + - - +
191K ILE 3.5 9.0 - - - +
192K ARG 3.2 0.2 - - - -
193K SER* 1.3 75.0 - - - +
195K MET* 1.3 64.4 + - - +
197K LEU* 3.2 21.1 + - - +
198K VAL* 3.0 40.6 + - - +
245K VAL* 4.1 11.5 - - + +
248K ARG* 2.9 31.1 + - - -
249K PHE* 3.7 23.1 - - + -
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Residues in contact with MET 195 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132K PHE* 3.8 23.1 - - + -
134K LEU* 4.1 17.3 - - + -
191K ILE* 3.1 32.1 + - + +
192K ARG* 3.0 18.0 + - - +
194K GLU* 1.3 77.3 - - - +
196K CYS* 1.3 56.6 + - - +
198K VAL 3.5 0.2 + - - -
199K MET* 2.9 45.2 + - + +
221K VAL* 4.6 5.2 - - + -
241K VAL* 3.6 13.5 - - + +
242K VAL* 3.7 41.3 - - + +
245K VAL* 3.7 16.2 - - + -
246K ALA 4.2 6.3 - - - +
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Residues in contact with CYS 196 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J PHE* 3.8 17.0 - - + -
34J PRO* 5.8 0.2 - - + -
192K ARG 2.9 16.7 + - - -
193K SER 3.1 7.6 + - - +
195K MET* 1.3 74.5 - - - +
197K LEU* 1.3 65.7 + - - +
199K MET* 3.2 2.7 + - - +
200K GLU* 3.0 30.1 + - - +
206K VAL* 3.7 34.8 - - + -
209K HIS* 3.7 25.6 - - - -
221K VAL* 3.7 17.9 - - - -
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Residues in contact with LEU 197 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J LYS* 4.5 21.3 - - + +
16J PHE* 3.5 25.4 - - + -
82J ASP* 3.3 30.1 - - + +
193K SER 2.9 18.5 + - - +
194K GLU* 3.2 19.0 + - - +
196K CYS* 1.3 76.4 - - - +
198K VAL* 1.3 60.0 + - + +
200K GLU* 3.3 11.3 + - - +
201K GLN* 3.0 41.4 + - - +
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Residues in contact with VAL 198 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78K PRO* 3.5 35.0 - - + -
79K PHE* 4.2 4.5 - - + -
194K GLU* 3.0 33.7 + - - +
197K LEU* 1.3 73.8 - - + +
199K MET* 1.3 65.8 + - - +
201K GLN* 3.0 20.0 + - - +
202K MET* 3.0 20.8 + - - +
241K VAL* 3.8 25.1 - - + -
245K VAL* 4.4 9.6 - - + -
248K ARG* 4.5 9.4 - - - +
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Residues in contact with MET 199 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195K MET* 2.9 31.1 + - + +
196K CYS 3.6 4.5 - - - +
198K VAL* 1.3 74.7 - - - +
200K GLU* 1.3 58.3 + - - +
202K MET* 2.9 19.8 + - - +
203K GLY 3.4 0.5 + - - -
204K LEU* 3.1 37.1 + - + +
206K VAL* 4.3 5.2 - - + -
221K VAL* 3.7 26.0 - - + -
223K THR* 4.2 7.0 - - - -
238K TYR* 3.5 45.3 - - + +
241K VAL* 3.8 22.0 - - + -
242K VAL* 3.6 27.4 - - + -
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Residues in contact with GLU 200 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J PRO* 4.6 2.8 - - - +
36J HIS* 2.6 37.5 + - - -
196K CYS* 3.0 19.8 + - - +
197K LEU* 3.6 11.8 - - - +
199K MET* 1.3 72.9 - - - +
201K GLN* 1.3 60.7 + - - +
202K MET 2.9 6.7 + - - -
203K GLY* 3.0 12.5 + - - -
204K LEU 3.3 19.6 - - - +
205K VAL* 4.0 2.7 - - - +
206K VAL* 3.0 30.5 + - + +
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Residues in contact with GLN 201 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75K VAL* 4.0 8.8 - - - +
76K ILE 5.4 0.3 - - - +
78K PRO* 4.3 17.3 - - + +
197K LEU* 3.0 34.3 + - - +
198K VAL* 3.0 20.5 + - - +
200K GLU* 1.3 75.2 - - - +
202K MET* 1.3 62.1 + - + +
203K GLY 3.4 2.1 + - - -
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Residues in contact with MET 202 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ARG* 5.1 0.9 - - - +
75K VAL* 3.8 29.7 - - + +
76K ILE 4.1 6.5 - - - +
78K PRO* 3.7 28.5 - - + -
86K ILE* 3.6 30.7 - - + -
198K VAL* 3.0 9.5 + - + +
199K MET* 2.9 10.8 + - - +
200K GLU 2.9 1.4 - - - -
201K GLN* 1.3 83.7 - - + +
203K GLY* 1.3 56.7 + - - +
204K LEU* 3.5 8.1 + - - +
237K ILE* 3.8 35.3 - - + +
240K TYR* 4.3 12.1 - - + -
241K VAL* 3.6 27.6 - - - -
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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