Contacts of the strand formed by residues 161 - 168 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A LEU* 5.6 0.7 - - - -
159B GLY 3.4 15.3 + - - +
160B SER* 1.3 75.6 - - - +
162B TYR* 1.3 62.9 + - - +
163B HIS* 4.3 9.5 + - + +
243B TYR* 3.8 4.2 - - - -
244B THR* 2.8 54.2 + - - +
249B THR* 3.8 4.3 + - + +
250B PRO 3.1 13.5 + - - +
251B PRO* 2.9 27.5 - - - +
252B VAL* 2.8 34.6 + - - +
285B ILE* 3.0 22.0 - - - +
286B MET* 3.5 15.0 + - - +
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Residues in contact with TYR 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A SER 4.3 0.2 - - - -
133A GLY* 3.6 16.7 - - - -
136A LEU* 3.9 17.3 - - + -
255A PHE* 3.3 35.3 - + - -
98B TRP* 4.7 0.8 - + - -
161B GLN* 1.3 74.8 - - - +
163B HIS* 1.3 65.9 + - - +
164B VAL* 3.8 10.9 - - + +
224B VAL* 3.2 34.4 - - + +
228B HIS* 3.5 14.2 + - - -
229B PRO* 4.5 6.9 - - - +
242B ASN 3.3 16.8 - - - -
243B TYR* 4.1 12.8 - + - -
244B THR* 4.9 0.2 - - - -
283B VAL* 3.2 29.4 - - + +
284B ASP* 3.2 2.8 - - - -
285B ILE* 2.6 52.8 + - + +
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Residues in contact with HIS 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 4.8 3.9 - - + +
161B GLN* 4.3 11.7 + - + +
162B TYR* 1.3 76.4 + - - +
164B VAL* 1.3 61.9 + - - +
241B GLY* 2.9 3.9 - - - -
242B ASN* 2.9 40.6 + - - +
244B THR* 5.9 0.9 - - - -
252B VAL 4.5 6.3 + - - -
253B LEU* 4.1 13.8 - - + +
283B VAL 2.7 9.6 - - - -
284B ASP* 2.8 32.8 + - + +
285B ILE 3.3 22.5 + - - -
286B MET* 3.4 30.0 - - - +
304B ARG* 4.5 7.9 - - - +
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 3.6 26.9 - - + -
98B TRP* 3.2 26.5 - - + -
162B TYR* 3.8 14.1 - - + +
163B HIS* 1.3 83.4 - - - +
165B PHE* 1.3 72.1 + - - +
229B PRO* 4.8 11.0 - - + -
239B TYR* 5.1 2.9 - - + -
240B PHE 3.0 16.6 - - - +
241B GLY* 3.3 12.6 - - - +
242B ASN 3.7 1.3 - - - +
282B CYS* 2.9 2.9 - - - +
283B VAL* 2.7 40.9 + - + +
284B ASP* 4.4 0.6 + - - -
304B ARG* 4.2 1.6 + - - +
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 4.7 0.4 - - - -
125B VAL* 5.1 9.6 - - + -
127B THR* 4.0 20.0 - - + -
164B VAL* 1.3 80.8 - - - +
166B ALA* 1.3 75.6 + - - +
167B VAL* 4.3 17.3 - - + -
239B TYR* 2.9 3.4 - - - -
240B PHE* 2.6 77.0 + + - -
261B THR* 5.9 3.6 - - + -
263B LEU* 6.0 0.4 - - + -
281B SER 3.0 14.1 - - - +
282B CYS* 3.2 12.3 - - + +
304B ARG* 3.1 34.3 - - - +
306B PHE* 4.4 8.3 - + + -
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Residues in contact with ALA 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B TRP* 5.8 0.7 - - + -
165B PHE* 1.3 80.6 - - - +
167B VAL* 1.3 70.4 + - - +
172B LEU* 4.4 12.1 - - + -
237B THR* 3.9 15.0 - - + -
238B ARG 2.8 14.1 - - - +
239B TYR* 3.2 14.6 - - + -
280B LEU* 3.7 2.1 - - - +
281B SER* 2.6 43.2 + - - +
306B PHE* 4.5 1.2 - - - -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ALA* 4.7 2.2 - - + -
125B VAL* 4.5 21.3 - - + -
165B PHE* 4.3 17.0 - - + -
166B ALA* 1.3 78.4 - - - +
168B GLY* 1.3 60.2 + - - +
237B THR* 3.2 4.6 - - - -
238B ARG* 2.7 28.7 + - - +
263B LEU* 3.8 31.6 - - + -
271B PRO* 3.7 11.3 - - + +
278B LEU* 4.2 18.6 - - + -
279B TYR 3.3 4.3 - - - -
280B LEU* 4.0 13.5 - - + -
306B PHE* 4.6 3.1 - - + -
308B ILE* 4.9 3.6 - - + -
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Residues in contact with GLY 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B VAL* 1.3 77.7 - - - +
169B GLY* 1.3 57.1 + - - -
170B GLU 3.1 8.1 - - - -
236B ASN 3.2 6.7 - - - -
237B THR* 3.2 19.0 - - - +
271B PRO* 4.1 5.2 - - - -
278B LEU* 3.6 7.7 - - - +
279B TYR* 2.8 45.6 + - - -
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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