Contacts of the strand formed by residues 176 - 184 (chain A) in PDB entry 1SOX
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 LYS 176 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ARG* 5.7 2.0 - - - +
174A PHE 3.3 2.9 + - - +
175A PRO* 1.3 71.7 - - - +
177A HIS* 1.3 67.8 + - - +
178A GLU* 4.1 23.3 + - - +
215A GLY* 5.1 2.2 - - - -
216A GLY 3.5 15.9 - - - +
272A TYR* 3.4 33.4 - - + +
273A GLU* 3.0 34.2 + - - +
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Residues in contact with HIS 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A PRO* 3.4 30.6 + - + -
176A LYS* 1.3 76.2 - - - +
178A GLU* 1.3 65.3 + - - +
179A VAL* 5.4 1.8 - - + -
215A GLY* 3.4 1.9 - - - -
216A GLY 2.9 31.5 + - - +
218A ARG* 3.5 55.8 + - + +
221A ASP* 4.4 2.4 + - - -
267A ASP* 6.1 0.7 - - - -
269A LEU* 3.7 14.2 - - + +
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Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LYS* 4.1 23.1 + - + +
177A HIS* 1.3 81.7 - - - +
179A VAL* 1.3 66.8 + - - +
213A ARG* 3.1 48.3 + - - +
214A TRP 3.0 10.8 - - - +
215A GLY* 4.2 8.5 - - - -
273A GLU* 4.7 3.6 - - - +
276A GLY* 6.0 1.4 - - - -
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Residues in contact with VAL 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A HIS* 5.3 1.8 - - + -
178A GLU* 1.3 80.5 - - - +
180A THR* 1.3 64.0 + - - +
181A ALA* 4.3 2.2 - - + -
213A ARG* 4.0 2.5 - - - +
214A TRP* 2.7 44.8 + - + +
267A ASP* 3.6 37.2 - - + +
269A LEU* 3.6 26.7 - - + -
290A VAL* 6.1 1.1 - - + -
292A PRO* 4.2 10.8 - - + -
408A TRP* 3.7 30.1 - - + -
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Residues in contact with THR 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PHE* 3.7 25.6 - - + -
129A LEU* 3.7 27.1 - - + +
179A VAL* 1.3 74.9 - - - +
181A ALA* 1.3 59.8 + - - +
211A THR* 4.0 7.6 - - + -
212A ALA 3.4 6.5 - - - +
213A ARG* 2.9 40.8 + - - +
408A TRP* 3.4 18.7 - - - +
409A ALA* 4.0 8.3 + - + +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A VAL* 3.7 4.1 + - + -
180A THR* 1.3 76.7 - - - +
182A THR* 1.3 64.1 + - - +
183A LEU* 3.9 2.8 + - + -
211A THR* 3.8 4.6 - - - -
212A ALA 3.0 19.7 + - - -
214A TRP* 3.2 32.6 + - + +
290A VAL* 4.5 4.3 - - + -
292A PRO* 4.2 25.4 - - + -
408A TRP* 3.7 17.9 - - + +
409A ALA 4.6 0.2 - - - +
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Residues in contact with THR 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ALA* 1.3 74.3 - - - +
183A LEU* 1.3 68.1 - - - +
184A GLN 4.0 1.8 + - - +
209A ILE* 3.4 37.5 - - + -
210A SER 3.4 5.6 - - - +
211A THR* 2.6 22.5 + - - +
291A VAL 5.8 0.2 - - - +
292A PRO* 5.7 0.5 - - - +
293A GLY 5.0 4.7 + - - -
294A VAL 5.2 2.3 - - - +
372A TRP* 3.6 37.7 - - + +
408A TRP 3.0 7.8 + - - +
409A ALA* 3.4 1.4 - - - -
410A TRP* 2.8 25.6 + - + -
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Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 4.1 12.1 - - + -
136A PHE* 3.3 12.5 - - + -
181A ALA* 3.9 2.4 + - + +
182A THR* 1.3 79.7 - - - +
184A GLN* 1.3 60.0 - - - +
209A ILE* 3.1 3.8 - - - +
210A SER 2.8 32.8 + - - +
214A TRP* 3.7 31.9 - - + +
288A ARG* 3.6 32.3 - - - +
290A VAL* 4.7 13.7 - - + -
291A VAL 4.9 7.6 - - - +
292A PRO* 6.1 0.2 - - + -
294A VAL 5.0 2.9 - - - +
296A GLY* 4.7 11.2 - - - -
299A SER* 3.7 21.3 - - - +
501A MTE 4.4 6.3 - - - +
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PHE* 4.4 0.4 - - - -
182A THR* 4.0 2.7 + - + -
183A LEU* 1.3 74.8 - - - +
185A CYS* 1.3 69.4 + - - +
188A ASN* 2.9 32.2 - - - +
208A ALA 3.6 11.7 - - - +
209A ILE* 3.9 17.4 - - + +
294A VAL 5.2 2.2 + - - -
296A GLY* 2.9 25.5 + - - +
345A LEU* 3.7 22.9 - - + +
346A PRO 5.0 0.3 - - - +
348A GLN* 3.1 31.3 + - - +
372A TRP* 3.4 32.4 - - + -
455A THR* 5.7 0.6 - - - +
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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