Contacts of the strand formed by residues 161 - 168 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D GLY 3.3 16.1 + - - +
160D SER* 1.3 76.5 - - - +
162D TYR* 1.3 62.8 + - - +
163D HIS* 4.1 8.6 + - + +
243D TYR* 3.7 3.9 - - - -
244D THR* 3.0 48.4 + - - +
249D THR* 3.5 3.8 + - + +
250D PRO 2.9 27.7 + - - -
251D PRO* 3.1 26.4 - - - +
252D VAL* 3.2 20.4 + - - +
285D ILE* 3.0 20.0 - - - +
286D MET* 3.6 18.4 + - - +
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Residues in contact with TYR 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C SER 4.2 0.9 - - - -
133C GLY* 3.5 18.8 - - - -
136C LEU* 3.7 25.6 - - + -
255C PHE* 3.3 40.7 - + - -
98D TRP* 4.5 6.3 - + - -
161D GLN* 1.3 75.8 - - - +
163D HIS* 1.3 69.8 + - - +
164D VAL* 3.8 13.7 - - + +
224D VAL* 3.6 22.6 - - + +
227D TRP 4.4 3.3 + - - -
228D HIS* 4.0 5.9 + - - -
229D PRO* 4.7 2.1 - - - +
242D ASN 3.4 12.1 - - - -
243D TYR* 4.2 15.3 - + + -
283D VAL* 3.3 31.5 - - + +
284D ASP* 3.2 1.7 - - - -
285D ILE* 2.5 45.4 + - + +
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Residues in contact with HIS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D VAL* 4.8 3.6 - - + +
161D GLN* 4.1 9.4 + - + +
162D TYR* 1.3 80.1 + - - +
164D VAL* 1.3 60.1 + - - +
165D PHE* 5.9 0.2 - - - -
241D GLY* 2.9 21.0 - - - -
242D ASN* 2.9 25.2 + - - +
244D THR* 5.8 1.1 - - - -
252D VAL 4.8 3.4 + - - -
253D LEU* 4.3 11.8 - - + +
283D VAL 3.0 6.5 - - - -
284D ASP* 2.8 35.9 + - + +
285D ILE 3.3 22.5 + - - -
286D MET* 3.4 32.6 - - + +
304D ARG* 4.7 7.6 - - - +
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Residues in contact with VAL 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C PHE* 3.7 24.9 - - + -
98D TRP* 3.0 31.9 - - + -
162D TYR* 3.8 24.5 - - + +
163D HIS* 1.3 73.7 - - - +
165D PHE* 1.3 71.4 + - - +
229D PRO* 4.9 9.9 - - + -
239D TYR* 5.1 2.9 - - + -
240D PHE 3.0 12.3 - - - +
241D GLY* 3.3 21.8 - - - -
242D ASN 4.1 0.7 - - - +
282D CYS* 3.0 4.6 - - - +
283D VAL* 3.0 27.7 + - + +
304D ARG* 4.2 2.7 + - - -
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Residues in contact with PHE 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D TRP* 5.5 0.2 - - - -
125D VAL* 4.7 11.0 - - + -
127D THR* 4.2 21.3 - - + -
164D VAL* 1.3 81.7 - - - +
166D ALA* 1.3 71.2 + - - +
167D VAL* 4.2 15.0 - - + -
239D TYR* 3.0 3.0 - - - +
240D PHE* 2.7 81.2 + + + -
261D THR* 5.4 6.3 - - + -
281D SER 3.0 14.8 - - - +
282D CYS* 3.3 11.0 - - + +
304D ARG* 4.1 23.3 - - - +
306D PHE* 4.4 12.1 - + + -
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Residues in contact with ALA 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D TRP* 6.0 1.3 - - + -
164D VAL* 5.9 0.4 - - + -
165D PHE* 1.3 83.0 - - - +
167D VAL* 1.3 67.4 + - - +
168D GLY 4.1 0.2 - - - -
172D LEU* 4.7 8.1 - - + -
237D THR* 3.9 13.7 - - + -
238D ARG 2.8 19.1 - - - +
239D TYR* 3.4 13.0 - - + -
279D TYR 3.5 3.7 - - - +
280D LEU* 3.7 3.1 - - - +
281D SER* 2.7 42.9 + - - +
306D PHE* 4.9 0.2 - - - -
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Residues in contact with VAL 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ALA* 4.7 7.4 - - + -
125D VAL* 4.2 11.2 - - + -
165D PHE* 4.2 17.9 - - + -
166D ALA* 1.3 81.8 - - - +
168D GLY* 1.3 59.6 + - - +
237D THR* 3.3 4.6 - - - -
238D ARG* 2.9 27.0 + - - +
240D PHE* 5.4 0.4 - - + -
263D LEU* 3.8 41.3 - - + -
271D PRO* 3.7 8.2 - - + +
278D LEU* 4.2 13.7 - - + -
279D TYR 3.5 2.2 - - - -
280D LEU* 4.0 19.7 - - + -
306D PHE* 5.0 0.4 - - + -
308D ILE* 4.6 7.2 - - + -
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Residues in contact with GLY 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D VAL* 1.3 76.0 - - - +
169D GLY* 1.3 58.0 + - - -
170D GLU 3.3 9.9 - - - -
236D ASN 3.3 5.8 - - - -
237D THR* 3.2 20.2 - - - +
271D PRO* 4.1 5.8 - - - -
273D CYS* 4.9 0.6 - - - -
278D LEU* 3.7 8.3 - - - +
279D TYR 2.8 41.0 + - - -
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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