Contacts of the strand formed by residues 140 - 150 (chain F) in PDB entry 3P6Y
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 140 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138F ASP* 4.1 8.3 + - + +
139F TRP* 1.3 73.0 - - - +
141F ILE* 1.3 60.8 + - - +
142F ASP* 4.1 19.2 + - - +
176F LEU 4.1 0.5 - - - +
177F VAL* 3.7 4.7 - - - +
178F GLN* 2.9 65.0 + - + +
180F GLN* 6.0 3.8 - - + +
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Residues in contact with ILE 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118F VAL* 4.0 29.6 - - + +
121F LEU* 3.9 27.6 - - + -
122F LYS* 3.7 33.4 + - + +
125F MET* 4.8 3.6 - - + -
139F TRP* 3.6 12.4 + - + -
140F VAL* 1.3 77.7 - - - +
142F ASP* 1.3 69.7 + - - +
175F PHE* 3.7 38.4 - - + -
176F LEU 3.9 4.7 - - - +
177F VAL* 3.9 20.9 - - + -
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Residues in contact with ASP 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ARG* 4.3 15.9 + - - +
140F VAL* 4.1 19.5 + - - +
141F ILE* 1.3 84.5 + - - +
143F ASP* 1.3 77.8 + - - +
144F CYS 4.3 0.9 + - - -
175F PHE* 5.2 2.9 - - - -
176F LEU 3.9 4.0 + - - -
178F GLN* 4.3 11.1 + - - +
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Residues in contact with ASP 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ARG* 3.4 41.4 + - - +
37F ILE* 4.4 3.8 - - - +
141F ILE 4.0 0.2 - - - -
142F ASP* 1.3 91.6 + - - +
144F CYS* 1.3 61.4 + - - +
145F ILE 3.7 0.3 + - - -
175F PHE* 3.4 7.6 - - - -
176F LEU* 2.8 41.5 + - + +
178F GLN* 3.8 10.2 + - - -
221F ARG* 4.0 17.8 + - - +
222F PHE* 4.3 14.3 - - + -
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Residues in contact with CYS 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E GLU* 5.8 7.4 - - - +
221E ARG* 3.5 31.9 + - + +
142F ASP 4.3 0.8 + - - -
143F ASP* 1.3 71.8 - - - +
145F ILE* 1.3 64.7 + - - +
146F GLY 3.5 25.4 - - - -
147F ASN* 4.4 7.2 - - - -
173F LYS* 3.7 25.1 - - - -
174F LEU 3.4 9.6 - - - -
175F PHE* 3.8 17.9 - - + -
221F ARG* 3.6 6.3 + - - +
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Residues in contact with ILE 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217E GLN 4.5 5.2 - - - +
218E LEU* 5.2 1.4 - - - +
221E ARG* 4.1 14.9 - - - +
83F VAL* 3.6 31.6 - - + -
143F ASP 3.9 8.1 - - - +
144F CYS* 1.3 77.7 - - - +
146F GLY* 1.3 60.2 + - - +
174F LEU* 2.9 27.3 + - + +
175F PHE 4.5 0.7 - - - +
176F LEU* 4.2 8.7 - - + +
215F LEU* 4.3 10.5 - - + -
218F LEU* 3.8 28.6 - - + +
219F LEU* 3.8 21.8 - - + -
221F ARG* 4.4 3.1 - - - +
222F PHE* 3.6 36.3 - - + -
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Residues in contact with GLY 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E SER* 3.5 11.4 - - - -
221E ARG* 4.2 3.3 - - - +
144F CYS* 3.5 8.2 - - - -
145F ILE* 1.3 83.5 - - - +
147F ASN* 1.3 72.7 + - - +
148F TRP* 4.5 10.3 - - - -
174F LEU* 3.2 28.7 + - - -
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Residues in contact with ASN 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E SER* 2.7 37.8 + - - +
221E ARG* 3.9 13.9 + - - +
222E PHE 5.0 2.6 + - - -
144F CYS* 4.4 4.2 - - - -
146F GLY* 1.3 78.8 + - - +
148F TRP* 1.3 62.9 + - - +
149F TRP* 3.6 23.9 - - + -
159F PRO* 3.4 23.7 - - - +
171F HIS* 3.2 23.6 + - - +
172F LYS 3.4 3.4 - - - -
173F LYS* 3.4 22.9 - - - +
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Residues in contact with TRP 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E TYR* 3.8 12.8 - + - -
217E GLN* 3.8 17.9 - - + +
220E SER* 4.9 2.2 + - - -
146F GLY* 4.5 6.0 - - - -
147F ASN* 1.3 87.2 + - - +
149F TRP* 1.3 62.6 + - - +
150F ARG 4.3 0.2 + - - -
157F GLN* 3.8 19.7 - - + +
158F TYR 3.3 24.7 - - - -
159F PRO* 3.5 27.4 - - + -
170F GLU 4.0 0.2 - - - +
171F HIS* 3.5 3.6 - - - -
172F LYS* 2.7 52.0 + - + +
174F LEU* 4.4 15.7 - - + +
210F PRO* 3.6 20.4 - - + -
211F ILE* 3.6 47.6 - - + +
214F SER* 3.5 20.0 - - - -
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Residues in contact with TRP 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220E SER* 4.9 3.6 - - - -
222E PHE 6.2 0.2 - - - -
76F MET* 4.9 3.4 - - - +
147F ASN* 3.6 37.9 - - + -
148F TRP* 1.3 74.7 - - - +
150F ARG* 1.3 58.7 + - - +
151F PRO* 3.4 9.0 - - + +
157F GLN* 3.4 4.1 - - - -
158F TYR* 2.9 30.5 + - - +
159F PRO 4.2 9.9 - - - -
160F TYR* 4.0 28.2 - - - +
161F ILE* 3.6 33.4 - - + +
162F PRO* 5.8 1.3 - - + -
168F PRO* 3.8 23.9 - - + +
170F GLU 3.4 14.4 - - - -
171F HIS* 3.6 35.8 + + + +
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Residues in contact with ARG 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F PHE* 3.9 8.4 - - - -
67F MET* 4.2 24.9 - - - +
148F TRP 4.3 0.4 + - - -
149F TRP* 1.3 71.6 - - - +
151F PRO* 1.3 63.1 - - + +
152F ASN 3.3 17.6 + - - +
154F GLU 3.1 28.1 + - - +
155F PRO* 3.1 23.0 + - - +
156F PRO 3.6 11.7 - - - +
157F GLN* 3.6 26.5 + - + +
168F PRO* 3.9 1.7 - - - -
169F LYS* 2.9 27.5 + - - +
170F GLU* 2.8 52.8 + - + -
172F LYS* 5.3 2.6 - - - +
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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