Contacts of the strand formed by residues 163 - 171 (chain C) in PDB entry 4A12
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 HIS 163 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C HIS* 3.1 29.1 + + + -
159C GLN* 3.4 2.1 - - - +
160C THR* 2.8 45.2 + - - +
162C LYS* 1.4 97.6 - - + +
164C TYR* 1.3 58.8 + - - +
165C TYR* 3.9 19.8 + - + -
183C LYS* 3.6 39.5 - - + -
184C MSE 3.3 4.3 - - - +
185C PHE* 3.7 25.5 - + + +
186C TYR* 3.4 7.9 - - - -
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Residues in contact with TYR 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ASN* 3.4 42.9 + - + +
126C ILE* 3.8 41.5 - - + -
128C GLN* 4.0 9.7 + - + -
156C VAL* 3.7 25.8 - - + -
158C ASN 3.7 1.8 - - - -
159C GLN* 3.0 36.8 + - + -
163C HIS* 1.3 70.1 - - - +
165C TYR* 1.3 63.9 + - - +
166C VAL* 3.8 1.4 + - + -
182C PHE 3.5 2.3 - - - +
184C MSE 2.7 39.4 + - + +
186C TYR* 3.4 46.9 - + + -
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Residues in contact with TYR 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156C VAL* 3.5 3.6 - - - -
157C VAL* 2.7 40.3 + - + -
158C ASN* 2.7 56.6 + - + +
159C GLN* 5.4 0.4 - - - -
160C THR* 3.9 18.7 + - + +
163C HIS* 3.9 15.1 + - + +
164C TYR* 1.3 76.1 - - - +
166C VAL* 1.3 55.2 + - - +
182C PHE 3.4 2.7 - - - +
183C LYS* 3.3 53.9 + - + -
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Residues in contact with VAL 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C CYS* 3.8 20.2 - - - -
125C LEU* 3.8 8.3 - - + -
126C ILE* 3.8 28.7 - - + -
154C ALA* 3.8 27.8 - - + -
155C ARG 3.4 11.2 - - - +
156C VAL* 4.4 12.6 - - + -
157C VAL* 4.7 1.1 - - - -
164C TYR 4.3 2.9 - - - +
165C TYR* 1.3 77.9 - - - +
167C GLU* 1.3 65.7 + - - +
168C VAL 4.1 0.2 - - - -
180C GLY 3.7 1.2 - - - +
181C ASN* 3.4 3.5 - - - +
182C PHE* 2.7 43.0 + - + +
184C MSE 4.0 10.8 - - + -
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Residues in contact with GLU 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLU 3.7 2.3 - - - +
154C ALA* 3.4 1.4 - - - -
155C ARG* 2.9 36.7 + - + +
157C VAL* 3.7 35.1 - - + +
165C TYR 4.4 0.2 - - - -
166C VAL* 1.3 71.1 - - - +
168C VAL* 1.3 62.2 + - - +
169C LYS* 3.5 25.7 + - - +
179C LYS* 6.5 1.1 - - + -
180C GLY 3.5 2.5 - - - +
181C ASN* 3.3 26.7 - - - +
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Residues in contact with VAL 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C ALA* 3.9 25.4 - - + +
121C LEU* 4.7 2.9 - - + -
122C CYS* 3.6 29.8 - - - -
152C ALA* 4.5 6.1 - - + -
153C GLU 3.4 11.7 - - - +
154C ALA* 3.8 11.4 - - + -
166C VAL* 4.3 1.1 - - + -
167C GLU* 1.3 76.1 - - - +
169C LYS* 1.3 65.1 + - - +
170C SER* 4.1 15.3 - - - +
178C PHE* 4.5 3.1 - - + -
179C LYS* 3.4 6.6 - - - +
180C GLY 2.7 38.4 + - - +
182C PHE* 3.8 18.8 - - + -
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Residues in contact with LYS 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C GLU* 2.9 40.9 + - + +
155C ARG* 4.5 15.3 - - - +
167C GLU* 3.5 29.5 + - - +
168C VAL* 1.3 78.7 - - - +
170C SER* 1.3 61.5 + - - +
171C TYR* 3.4 33.1 - - + +
176C LEU* 3.8 15.3 - - + -
178C PHE 3.6 3.8 - - - -
179C LYS* 4.3 21.5 - - + +
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Residues in contact with SER 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C LEU* 4.8 3.3 + - - +
117C GLN* 4.4 1.9 + - - -
118C ALA* 5.3 0.9 - - - +
150C VAL* 3.6 22.7 - - - +
151C ARG 3.4 4.3 - - - -
152C ALA* 3.3 20.6 - - - +
168C VAL* 4.1 3.3 - - - +
169C LYS* 1.3 72.8 - - - +
171C TYR* 1.3 59.4 + - - +
176C LEU* 3.6 5.5 - - - +
177C VAL* 3.0 25.5 + - - -
178C PHE* 2.9 42.0 + - - +
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Residues in contact with TYR 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C THR 3.7 0.7 - - - +
150C VAL* 3.5 4.9 - - - -
151C ARG* 2.8 76.6 + - - +
153C GLU* 3.3 24.7 + - + -
169C LYS* 3.4 42.4 - - + +
170C SER* 1.3 73.0 - - - +
172C VAL* 1.3 63.6 + - - +
173C LYS 4.2 0.4 - - - -
174C HIS* 4.3 7.9 - - + -
175C THR 3.3 15.9 - - - +
176C LEU* 3.5 40.6 - - + +
177C VAL* 4.1 0.7 - - - -
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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