Contacts of the strand formed by residues 237 - 244 (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 THR 237 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ASN* 3.0 13.5 + - - -
166B ALA* 3.9 12.8 - - + -
167B VAL 3.2 14.4 - - - +
168B GLY* 3.2 29.2 - - - +
170B GLU* 4.2 8.0 + - - +
171B PRO 3.9 13.5 + - - -
172B LEU* 4.3 15.6 - - + +
173B ASP* 4.5 1.7 + - - -
235B GLU* 3.5 28.1 + - - +
236B ASN* 1.3 81.8 + - - +
238B ARG* 1.3 74.7 + - - +
239B TYR* 5.1 1.6 - - - -
279B TYR* 4.8 2.0 - - + +
281B SER* 5.0 1.6 - - - +
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Residues in contact with ARG 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ASN* 2.8 12.4 + - - +
258A THR* 5.0 11.0 - - - -
166B ALA* 2.8 3.5 - - - +
167B VAL* 2.7 33.6 + - + +
235B GLU* 4.1 11.1 + - - +
236B ASN* 4.0 5.7 + - - +
237B THR* 1.3 100.6 + - - +
239B TYR* 1.3 61.8 + - - +
240B PHE* 4.3 18.7 - - + -
262B VAL 4.8 1.8 - - - +
263B LEU* 2.6 43.4 + - + +
264B LEU 4.0 7.0 + - - -
265B ASP* 3.0 32.1 + - - +
270B GLY 3.3 25.4 + - - -
271B PRO* 4.2 10.9 - - + +
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Residues in contact with TYR 239 (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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128A GLU* 2.8 34.1 + - - -
255A PHE* 4.2 2.0 - - + -
256A THR* 2.6 31.0 + - - -
257A ASN* 2.9 50.7 - - + +
98B TRP* 6.3 0.4 - - + -
164B VAL* 5.1 3.4 - - + -
165B PHE 2.9 8.7 - - - +
166B ALA* 3.2 20.9 - - + -
172B LEU* 4.9 5.6 - - + -
229B PRO* 3.6 36.3 - - + -
230B ASP 4.6 9.4 - - - -
231B PRO* 3.8 18.3 - - + +
235B GLU* 4.8 13.0 - - - -
237B THR 4.9 3.6 - - - -
238B ARG* 1.3 76.6 - - - +
240B PHE* 1.3 72.0 - - - +
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Residues in contact with PHE 240 (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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255A PHE* 3.0 11.0 - - - +
256A THR* 3.2 9.4 - - - +
258A THR* 3.1 38.4 - - + -
125B VAL* 6.2 0.2 - - + -
164B VAL* 3.0 5.9 - - - -
165B PHE* 2.6 88.5 + + - +
238B ARG* 4.3 12.8 - - + -
239B TYR* 1.3 95.3 - - - +
241B GLY* 1.3 58.2 + - - +
261B THR* 4.9 18.2 - - + -
262B VAL 6.0 2.5 - - - -
263B LEU* 5.3 5.8 - - + -
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Residues in contact with GLY 241 (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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254A GLN* 3.6 3.3 - - - +
255A PHE* 2.7 36.8 + - - +
163B HIS 2.9 15.7 - - - -
164B VAL* 3.3 4.9 - - - -
240B PHE* 1.3 80.5 - - - +
242B ASN* 1.3 61.0 + - - +
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Residues in contact with ASN 242 (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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252A VAL* 4.5 3.6 - - - +
253A LEU 3.0 19.3 - - - +
254A GLN* 3.3 14.1 + - - +
255A PHE* 4.3 6.1 - - - +
161B GLN 3.9 0.3 - - - +
162B TYR* 3.3 28.8 - - - -
163B HIS* 2.9 31.8 + - - +
164B VAL* 3.7 2.0 - - - +
241B GLY* 1.3 77.4 - - - +
243B TYR* 1.3 67.1 + - - +
244B THR* 3.5 14.1 + - - +
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Residues in contact with TYR 243 (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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132A SER* 3.2 42.7 - - - -
135A LEU* 3.3 35.7 + - + +
136A LEU* 3.6 24.9 - - + -
156A PRO* 4.8 3.8 - - - +
157A VAL 5.0 0.5 + - - -
251A PRO* 3.2 27.7 - - + +
252A VAL* 3.0 24.5 - - - +
253A LEU* 3.0 17.0 + - + +
286A MET* 6.0 1.1 - - + -
160B SER* 3.5 6.5 + - - -
161B GLN 3.8 5.8 - - - -
162B TYR* 4.1 12.1 - + + -
242B ASN* 1.3 75.8 - - - +
244B THR* 1.3 73.9 + - - +
245B GLY* 2.7 36.2 - - - -
246B GLY 3.9 1.2 + - - -
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Residues in contact with THR 244 (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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250A PRO* 5.4 2.0 - - + -
251A PRO 3.2 4.9 - - - +
252A VAL* 3.5 22.0 - - + -
160B SER* 3.1 5.5 - - - -
161B GLN* 2.8 57.4 + - + +
163B HIS* 5.9 1.0 - - - -
242B ASN* 3.5 12.7 + - - +
243B TYR* 1.3 80.4 - - - +
245B GLY* 1.3 62.1 + - - +
249B THR* 4.8 10.3 - - + +
252B VAL* 6.5 1.3 - - + -
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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
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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