Contacts of the strand formed by residues 161 - 168 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F GLY 3.2 16.6 + - - +
160F SER* 1.3 74.5 - - - +
162F TYR* 1.3 64.4 + - - +
163F HIS* 4.4 9.6 + - + +
242F ASN 4.4 0.2 - - - -
243F TYR* 3.7 4.0 - - - -
244F THR* 2.8 52.9 + - - +
249F THR* 3.4 5.7 + - + +
250F PRO 3.1 13.1 + - - +
251F PRO* 3.0 41.6 - - - +
252F VAL* 3.2 17.3 + - - +
285F ILE* 3.2 15.7 - - - +
286F MET* 3.4 18.5 + - - +
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Residues in contact with TYR 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F TRP* 4.5 7.3 - + - -
161F GLN* 1.3 75.7 - - - +
163F HIS* 1.3 66.1 + - - +
164F VAL* 3.4 24.5 - - + +
224F VAL* 3.4 33.7 - - + +
227F TRP 4.3 4.5 + - - -
228F HIS* 4.1 19.2 + + - +
229F PRO* 4.8 6.1 - - - +
242F ASN* 3.5 8.5 - - - -
243F TYR* 4.0 35.0 - + + -
283F VAL* 3.2 22.3 - - + +
284F ASP* 3.2 1.7 - - - -
285F ILE* 2.6 51.3 + - + +
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Residues in contact with HIS 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F VAL* 4.9 5.5 - - + +
161F GLN* 4.4 9.4 + - + +
162F TYR* 1.3 73.3 - - - +
164F VAL* 1.3 71.2 + - - +
241F GLY* 2.9 15.3 - - - -
242F ASN* 3.0 20.3 + - - +
244F THR* 6.1 0.7 - - - -
252F VAL 4.9 2.4 + - - -
253F LEU* 4.0 19.5 - - + +
283F VAL* 2.7 9.0 - - - -
284F ASP* 2.9 37.6 + - + +
285F ILE 3.3 24.8 + - - -
286F MET* 3.6 24.5 - - - +
304F ARG* 4.3 9.6 - - - +
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Residues in contact with VAL 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F TRP* 3.5 19.1 - - + -
162F TYR* 3.4 30.3 - - + +
163F HIS* 1.3 86.3 - - - +
165F PHE* 1.3 74.8 + - - +
229F PRO* 5.0 7.4 - - + -
239F TYR* 4.7 10.8 - - + -
240F PHE 2.9 21.5 - - - +
241F GLY* 3.6 9.4 - - - -
242F ASN* 3.9 4.7 - - - +
282F CYS* 3.0 2.9 - - - +
283F VAL* 2.7 37.4 + - + +
284F ASP* 4.2 0.2 + - - -
304F ARG* 3.9 1.7 + - - +
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Residues in contact with PHE 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F TRP* 4.8 2.0 - - - -
125F VAL* 5.2 10.5 - - + -
127F THR* 4.3 22.9 - - + -
164F VAL* 1.3 83.6 - - - +
166F ALA* 1.3 82.0 + - - +
167F VAL* 4.7 9.4 - - + -
239F TYR* 3.0 4.1 - - - +
240F PHE* 2.7 79.6 + + + +
241F GLY* 5.6 0.4 - - - -
261F THR* 6.0 4.7 - - + -
281F SER 2.9 15.7 - - - +
282F CYS* 3.4 11.4 - - + +
304F ARG* 4.1 25.4 - - - +
306F PHE* 4.2 14.1 - + + -
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Residues in contact with ALA 166 (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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98F TRP* 6.1 1.1 - - + -
165F PHE* 1.3 85.6 - - - +
167F VAL* 1.3 64.2 + - - +
168F GLY 3.9 0.2 - - - -
172F LEU* 4.9 6.1 - - + -
237F THR* 3.6 14.8 - - + -
238F ARG 2.7 20.6 - - - +
239F TYR* 3.2 12.8 - - + +
279F TYR 3.3 3.8 - - - +
280F LEU* 3.6 2.4 - - - -
281F SER* 2.7 35.9 + - - +
306F PHE* 4.4 1.4 - - - -
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Residues in contact with VAL 167 (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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122F ALA* 4.2 10.8 - - + -
125F VAL* 4.0 30.5 - - + -
165F PHE* 4.7 6.4 - - + -
166F ALA* 1.3 76.8 - - - +
168F GLY* 1.3 60.7 + - - +
237F THR* 3.3 4.1 - - - -
238F ARG* 2.9 24.4 + - - +
263F LEU* 4.0 29.4 - - + -
271F PRO* 3.7 8.8 - - + +
278F LEU* 3.7 24.0 - - + -
279F TYR 3.5 2.2 - - - -
280F LEU* 4.1 11.0 - - + -
306F PHE* 4.5 8.3 - - + -
308F ILE* 4.7 3.4 - - + -
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Residues in contact with GLY 168 (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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167F VAL* 1.3 74.6 - - - +
169F GLY* 1.3 55.5 + - - -
170F GLU 3.4 8.5 - - - -
236F ASN 3.5 6.3 - - - -
237F THR* 3.0 22.6 - - - +
271F PRO* 4.4 4.9 - - - -
273F CYS* 5.3 0.5 - - - -
278F LEU* 3.6 9.0 - - - +
279F TYR 2.7 43.7 + - - -
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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