Contacts of the strand formed by residues 161 - 168 (chain C) in PDB entry 1SID
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 GLN 161 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B LEU* 5.3 0.7 - - - -
159C GLY 3.7 11.7 + - - -
160C SER* 1.3 73.2 - - - +
162C TYR* 1.3 64.1 + - - +
163C HIS* 4.2 6.3 + - + +
243C TYR* 3.7 4.7 - - - -
244C THR* 2.9 50.2 + - - +
249C THR* 3.9 4.9 + - - +
250C PRO 3.1 14.4 + - - -
251C PRO* 3.0 26.8 - - - +
252C VAL* 3.3 30.3 + - - +
285C ILE* 3.0 22.4 - - - +
286C MET* 3.3 26.2 + - + +
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Residues in contact with TYR 162 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLY* 3.8 19.1 - - - -
136B LEU* 3.9 15.0 - - + -
255B PHE* 3.3 36.0 - + - -
98C TRP* 4.5 8.1 - + - -
161C GLN* 1.3 76.5 - - - +
163C HIS* 1.3 68.2 + - - +
164C VAL* 3.6 13.3 - - + +
224C VAL* 3.2 32.1 - - + +
227C TRP 4.6 0.7 + - - -
228C HIS* 4.3 4.2 + - - -
229C PRO* 4.9 0.3 - - - +
242C ASN 3.3 18.4 - - - -
243C TYR* 3.9 16.6 - + + -
244C THR* 4.7 0.2 - - - -
283C VAL* 3.4 20.6 - - + +
284C ASP* 3.2 1.4 - - - -
285C ILE* 2.5 66.7 + - + +
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Residues in contact with HIS 163 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C VAL* 5.0 3.5 - - + +
161C GLN* 4.2 9.0 + - + -
162C TYR* 1.3 83.2 + - - +
164C VAL* 1.3 62.8 + - - +
241C GLY* 2.8 20.3 - - - -
242C ASN* 2.8 30.0 + - - +
244C THR* 5.7 0.7 - - - -
252C VAL 4.7 2.5 + - - -
253C LEU* 4.3 11.5 - - + +
283C VAL 2.8 5.6 - - - -
284C ASP* 3.0 35.7 + - + +
285C ILE 3.2 14.3 + - - -
286C MET* 3.2 41.0 - - + +
304C ARG* 4.5 8.7 - - - +
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Residues in contact with VAL 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 4.1 13.7 - - + -
98C TRP* 3.9 17.9 - - + -
162C TYR* 3.6 36.3 - - + +
163C HIS* 1.3 80.4 - - - +
165C PHE* 1.3 64.9 - - - +
229C PRO* 4.9 4.5 - - + -
239C TYR* 4.7 7.9 - - + -
240C PHE 2.9 31.6 - - - +
241C GLY* 3.7 7.0 - - - +
242C ASN 4.2 0.9 - - - +
282C CYS* 2.9 5.1 - - - +
283C VAL* 2.7 37.5 + - + +
304C ARG* 4.0 2.2 + - - -
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Residues in contact with PHE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C TRP* 5.2 1.6 - - - -
125C VAL* 4.8 9.2 - - + -
127C THR* 4.1 21.8 - - + -
163C HIS 6.0 0.2 - - - -
164C VAL* 1.3 79.3 - - - +
166C ALA* 1.3 68.0 + - - +
167C VAL* 4.2 12.3 - - + -
239C TYR* 3.0 2.7 - - - -
240C PHE* 2.7 88.1 + + + -
261C THR* 5.7 7.2 - - + -
281C SER 3.0 8.3 - - - +
282C CYS* 3.3 17.0 - - + +
304C ARG* 3.8 27.1 - - - +
306C PHE* 4.0 17.0 - + + -
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Residues in contact with ALA 166 (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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98C TRP* 6.1 1.8 - - + -
165C PHE* 1.3 76.7 - - - +
167C VAL* 1.3 66.6 + - - +
172C LEU* 4.8 7.4 - - + -
237C THR* 3.7 17.0 - - + -
238C ARG 2.7 18.2 - - - +
239C TYR* 3.5 14.8 - - + -
279C TYR 3.4 3.4 - - - +
280C LEU* 3.5 3.5 - - - +
281C SER* 2.6 42.8 + - - +
306C PHE* 4.5 1.7 - - - -
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Residues in contact with VAL 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C ALA* 4.7 7.9 - - + -
125C VAL* 4.1 17.7 - - + -
165C PHE* 4.2 13.9 - - + -
166C ALA* 1.3 79.5 - - - +
168C GLY* 1.3 59.9 + - - +
237C THR* 3.3 3.7 - - - -
238C ARG* 2.8 26.9 + - - +
263C LEU* 4.0 38.8 - - + -
271C PRO* 3.9 7.7 - - + +
278C LEU* 4.0 12.6 - - + -
279C TYR 3.4 2.2 - - - -
280C LEU* 3.8 21.3 - - + -
306C PHE* 4.8 1.3 - - + -
308C ILE* 4.6 7.6 - - + -
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Residues in contact with GLY 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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167C VAL* 1.3 77.2 - - - +
169C GLY* 1.3 59.2 + - - -
170C GLU 3.4 4.9 - - - -
236C ASN 3.5 5.4 - - - -
237C THR* 3.1 18.7 - - - +
271C PRO* 4.3 6.1 - - - -
273C CYS* 5.3 0.8 - - - -
278C LEU* 3.6 7.0 - - - +
279C TYR* 2.6 46.3 + - - +
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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
------------------------------------------------------------
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