Contacts of the helix formed by residues 189 - 202 (chain A) in PDB entry 3FTC
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 ASP 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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187A VAL* 3.6 8.6 - - - +
188A LYS* 1.3 83.2 - - + +
190A LEU* 1.3 56.8 + - - +
191A LYS* 3.0 23.7 + - - +
192A ASN* 3.0 23.4 + - + +
193A TYR 3.0 22.2 + - - -
240A TYR* 3.7 3.9 + - - +
244A GLU* 4.5 1.0 + - - -
245A ASP* 5.6 5.2 - - - +
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A VAL 4.2 6.3 - - - +
116A TYR* 3.4 48.6 - - + +
118A LYS* 4.4 14.8 - - - -
119A ASP* 5.8 2.7 - - - +
148A PHE* 3.7 16.1 - - + -
152A PHE* 3.3 43.1 - - + -
187A VAL* 4.2 7.4 - - + +
188A LYS 4.1 1.1 + - - +
189A ASP* 1.3 70.4 + - - +
191A LYS* 1.3 61.3 + - + +
193A TYR* 3.3 5.7 + - - +
194A LYS* 2.9 29.3 + - - +
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Residues in contact with LYS 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A TYR* 4.5 19.5 - - + -
189A ASP* 3.0 10.8 + - - +
190A LEU* 1.3 77.6 - - + +
192A ASN* 1.3 58.1 + - - +
194A LYS* 3.5 8.1 + - - +
195A LYS* 3.1 27.0 + - - +
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Residues in contact with ASN 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ASP* 3.0 31.2 + - + +
191A LYS* 1.3 75.4 - - - +
193A TYR* 1.3 59.2 + - - +
195A LYS* 3.3 18.9 + - - +
196A PHE* 2.9 26.4 + - - +
240A TYR* 2.8 30.4 + - - +
243A ILE* 5.6 4.8 + - - +
244A GLU* 5.6 5.1 - - - +
245A ASP 6.0 0.6 - - - +
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Residues in contact with TYR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.0 10.0 - - - +
148A PHE* 3.8 24.0 - + - -
151A THR* 2.7 43.5 + - + -
152A PHE* 4.2 4.9 - + - -
185A PHE* 5.7 0.2 - + - -
187A VAL* 3.5 30.1 - - + -
189A ASP 3.0 5.8 + - - +
190A LEU 3.6 7.0 - - - +
191A LYS 3.3 0.2 - - - -
192A ASN* 1.3 77.5 - - - +
194A LYS* 1.3 57.0 + - - +
196A PHE* 3.2 29.6 + + - +
197A LEU* 3.0 44.2 + - + +
236A PHE* 4.5 2.8 - - - +
237A PHE* 3.6 17.5 - + - -
240A TYR* 3.5 35.6 + + + +
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Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLU* 2.6 25.7 + - - +
116A TYR* 3.0 23.9 + - + +
144A TRP* 3.6 29.7 - - + -
148A PHE* 4.2 16.5 - - + -
190A LEU 2.9 18.1 + - - +
191A LYS* 3.6 7.0 - - - +
193A TYR* 1.3 73.6 - - - +
195A LYS* 1.3 56.0 + - - +
197A LEU* 3.3 5.0 + - - +
198A THR* 2.8 48.6 + - + +
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A LYS 3.1 12.5 + - - +
192A ASN* 3.4 21.2 + - - +
194A LYS* 1.3 79.5 - - - +
196A PHE* 1.3 56.1 + - - +
198A THR* 2.8 20.4 + - - +
199A LYS* 2.9 51.0 + - + +
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Residues in contact with PHE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A ASN* 2.9 13.6 + - - +
193A TYR* 3.3 21.8 - + - +
195A LYS* 1.3 74.6 - - - +
197A LEU* 1.3 80.6 + - + +
199A LYS* 3.5 9.1 + - - +
200A ILE* 3.2 27.0 + - + +
212A ILE* 5.7 3.6 - - + -
236A PHE* 3.6 36.1 - + + -
239A LEU* 3.5 34.1 - - + -
240A TYR* 3.5 31.2 - + + -
243A ILE* 3.7 26.7 - - + -
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Residues in contact with LEU 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TRP* 3.8 17.9 - - + +
147A VAL* 3.7 12.1 - - + -
148A PHE* 3.6 47.3 - - + +
193A TYR* 3.0 34.5 + - + +
194A LYS* 3.7 4.3 - - - +
196A PHE* 1.3 86.9 - - + +
198A THR* 1.3 59.9 + - - +
200A ILE* 3.1 6.6 - - - +
201A PHE* 3.0 32.6 + - + -
236A PHE* 3.6 34.1 - - + -
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Residues in contact with THR 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A TRP* 4.0 28.9 - - + +
194A LYS* 2.8 45.1 + - + +
195A LYS* 2.8 26.5 + - - +
197A LEU* 1.3 71.8 - - - +
199A LYS* 1.3 56.2 + - - +
201A PHE* 4.3 1.9 - - - +
202A GLN* 2.9 42.7 + - - +
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Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LYS* 2.9 49.0 + - + +
196A PHE* 3.8 7.9 - - - +
198A THR* 1.3 76.7 + - - +
200A ILE* 1.3 62.3 + - - +
202A GLN* 3.7 13.8 + - - +
211A LYS* 3.6 20.2 - - + +
212A ILE* 5.4 4.7 - - + -
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Residues in contact with ILE 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A PHE* 3.2 16.4 + - + +
197A LEU* 3.1 18.6 - - + +
199A LYS* 1.3 77.9 - - - +
201A PHE* 1.3 56.8 + - + +
208A LEU* 3.7 21.5 - - + +
211A LYS* 2.8 30.6 + - - +
212A ILE* 3.8 20.6 - - + +
217A LEU* 5.4 0.4 - - + -
228A VAL* 3.9 11.4 - - + +
231A LEU* 3.8 23.3 - - + -
236A PHE* 3.7 26.0 - - + -
239A LEU* 3.8 27.4 - - + -
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Residues in contact with PHE 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A THR* 3.3 27.4 - - + -
143A GLY* 3.6 15.9 - - - -
144A TRP* 3.6 29.6 - - + +
147A VAL* 3.9 13.2 - - + -
197A LEU* 3.0 28.7 + - + +
198A THR* 4.3 1.8 - - - +
200A ILE* 1.3 79.2 - - + +
202A GLN* 1.3 66.9 + - - +
203A ASN 3.5 1.2 + - - -
204A ARG* 3.6 35.7 + - - +
211A LYS* 3.9 1.7 + - - +
228A VAL* 3.5 30.4 - - + +
229A GLU* 6.3 0.2 - - - -
236A PHE* 3.5 31.0 - + - -
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Residues in contact with GLN 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A THR* 2.9 29.0 + - - +
199A LYS* 3.8 11.2 - - - +
200A ILE 3.5 0.4 - - - -
201A PHE* 1.3 73.4 - - - +
203A ASN* 1.3 79.3 + - - +
211A LYS* 2.6 35.0 + - + +
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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