Contacts of the strand formed by residues 182 - 191 (chain F) in PDB entry 3KYM
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 TYR 182 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F LEU* 6.1 0.3 - - - +
116F THR* 5.0 10.7 - - + +
150F ASP* 3.2 4.7 + - - -
151F TYR* 2.8 54.7 + - + +
152F PHE* 3.8 32.7 - + - -
153F PRO* 4.5 1.8 - - + -
154F GLU* 3.5 47.8 + - + +
174F ALA* 3.9 19.7 - - + -
175F VAL 3.6 13.7 - - - -
176F LEU* 3.9 31.0 - - + +
181F LEU* 1.3 75.1 - - - +
183F SER* 1.3 65.7 - - - +
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Residues in contact with SER 183 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178E THR* 6.0 1.4 - - - +
147F LEU* 4.2 8.5 - - - +
148F VAL 3.1 15.4 + - - -
149F LYS* 3.5 26.2 - - - +
151F TYR* 3.8 2.7 - - - -
174F ALA* 4.8 0.7 - - - -
175F VAL* 3.3 25.9 + - - +
177F GLN* 3.7 18.3 + - - +
182F TYR* 1.3 79.8 - - - +
184F LEU* 1.3 67.1 + - - +
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Residues in contact with LEU 184 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F LEU* 3.3 6.3 - - - +
148F VAL* 2.7 56.7 + - + -
151F TYR* 4.0 21.8 - - + +
156F VAL* 4.5 17.7 - - + +
158F VAL* 5.1 2.7 - - + -
171F THR* 4.3 15.7 - - + -
172F PHE* 3.1 28.3 - - + +
173F PRO* 4.1 3.6 - - + +
174F ALA* 4.0 16.2 - - + +
183F SER* 1.3 76.6 + - - +
185F SER* 1.3 67.6 + - - +
186F SER 4.7 0.4 - - - +
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Residues in contact with SER 185 (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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133E VAL* 4.3 11.2 - - - +
176E SER* 4.8 6.2 + - - -
178E THR* 5.7 2.2 - - - -
130F LEU* 3.0 32.2 - - - +
146F CYS 3.4 5.7 + - - -
147F LEU* 3.5 12.2 - - - +
171F THR* 3.9 0.5 - - - -
172F PHE* 3.1 49.3 + - - +
184F LEU* 1.3 78.6 - - - +
186F SER* 1.3 57.9 + - - +
187F VAL* 4.6 2.0 - - - -
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Residues in contact with SER 186 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145F GLY* 3.1 3.0 - - - -
146F CYS* 2.8 36.5 + - - +
148F VAL* 5.8 0.7 - - - -
158F VAL* 3.6 21.2 - - - +
160F TRP* 3.2 23.7 + - - -
169F VAL* 4.6 0.3 - - - +
170F HIS 3.4 5.8 + - - -
171F THR* 2.8 32.9 + - - +
184F LEU* 4.7 2.0 - - - +
185F SER* 1.3 72.9 - - - +
187F VAL* 1.3 64.2 + - - +
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Residues in contact with VAL 187 (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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118E PHE* 4.9 3.8 - - + -
133E VAL* 6.0 1.8 - - + -
135E LEU* 3.7 37.0 - - + -
137E ASN* 4.8 2.7 - - - +
130F LEU* 4.3 18.8 - - + -
144F LEU 3.3 13.0 - - - +
145F GLY* 4.0 0.7 - - - -
160F TRP* 4.8 0.9 - - - -
168F GLY 3.9 0.4 - - - +
169F VAL* 3.4 4.5 - - - +
170F HIS* 2.7 51.0 + - + +
172F PHE* 3.7 25.4 - - + -
185F SER* 4.4 2.5 - - - +
186F SER* 1.3 84.4 + - - +
188F VAL* 1.3 62.2 + - - +
189F THR* 5.8 0.9 - - + +
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Residues in contact with VAL 188 (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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142F ALA 3.9 0.5 - - - +
143F ALA* 3.6 2.6 - - - -
144F LEU* 2.8 55.8 + - + +
160F TRP* 3.7 27.1 - - + -
165F LEU* 3.7 24.5 - - + -
167F SER 4.4 5.2 - - - +
168F GLY 3.5 4.7 - - - +
169F VAL* 4.1 17.5 - - + -
187F VAL* 1.3 78.4 - - - +
189F THR* 1.3 74.3 + - - +
190F VAL* 4.3 9.4 - - + +
200F TYR* 5.0 2.0 - - + -
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Residues in contact with THR 189 (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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116E PHE* 4.7 7.9 - - + -
135E LEU* 5.4 1.1 - - + -
137E ASN* 3.3 37.5 + - + +
138E ASN* 5.3 1.4 + - - +
141F THR* 5.1 9.4 - - - +
142F ALA 3.4 8.3 - - - -
143F ALA* 4.4 13.0 - - + +
167F SER 4.1 7.8 - - - +
168F GLY* 3.2 22.2 + - - +
187F VAL* 6.1 0.9 - - + -
188F VAL* 1.3 78.3 - - - +
190F VAL* 1.3 73.5 + - - +
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Residues in contact with VAL 190 (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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141F THR* 4.2 3.1 - - - -
142F ALA* 2.7 34.0 + - - +
144F LEU* 5.0 1.6 - - + -
165F LEU* 4.8 9.9 - - + -
167F SER 5.0 2.2 - - - +
188F VAL* 4.3 13.2 - - + +
189F THR* 1.3 83.8 - - - +
191F PRO* 1.3 76.6 - - + +
194F ASN* 5.4 2.0 - - + +
195F PHE* 3.1 37.8 - - + -
200F TYR* 3.4 36.3 - - + +
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Residues in contact with PRO 191 (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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140F SER 3.4 15.5 - - - +
141F THR* 3.8 15.0 - - + -
190F VAL* 1.3 89.0 - - + +
192F SER* 1.3 61.8 + - - +
193F SER* 3.6 7.0 + - - +
194F ASN* 3.7 29.2 + - - +
195F PHE* 3.2 17.1 + - - -
79K GLN* 3.8 24.7 - - + +
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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