Contacts of the helix formed by residues 175 - 188 (chain A) in PDB entry 1YG1
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 LEU 175 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A THR 2.7 26.2 - - - +
172A VAL* 2.7 21.8 - - - +
173A GLY 3.0 1.2 + - - -
174A ILE* 1.3 91.8 - - + +
176A VAL* 1.3 63.1 + - + +
177A ALA 3.0 2.1 + - - -
178A GLN* 3.4 8.3 + - - +
179A ILE* 3.8 4.7 + - + -
314A VAL* 4.3 2.4 - - + +
318A THR* 2.8 50.4 - - + +
319A ALA* 4.6 5.2 - - - +
321A THR* 2.8 28.0 - - - +
322A GLY* 3.2 22.4 - - - +
325A ASN* 5.2 0.4 - - - +
381A ILE* 5.2 3.8 - - + -
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Residues in contact with VAL 176 (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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31A GLN* 5.6 1.6 - - - +
35A ASN* 4.4 13.5 - - - +
172A VAL 4.7 3.1 - - - +
173A GLY* 3.1 25.1 + - - +
174A ILE 3.2 0.4 + - - -
175A LEU* 1.3 75.5 - - + +
177A ALA* 1.3 62.5 + - - +
179A ILE* 2.7 36.6 - - + +
180A PHE* 2.8 19.9 + - + +
198A LEU* 4.8 3.4 - - + -
201A VAL* 5.9 7.9 - - + -
202A PRO* 6.5 1.1 - - + -
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Residues in contact with ALA 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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35A ASN* 4.5 17.5 - - - +
38A ALA* 4.6 4.3 - - + -
41A SER* 4.7 11.5 + - - -
174A ILE 4.0 6.9 + - - +
175A LEU 3.0 2.2 + - - -
176A VAL* 1.3 77.3 - - - +
178A GLN* 1.3 60.5 + - + +
180A PHE 3.3 0.2 + - - -
181A GLY* 2.8 26.0 + - - -
198A LEU* 3.0 42.6 - - + +
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Residues in contact with GLN 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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41A SER* 3.2 27.4 + - - +
44A LEU* 4.6 2.1 - - - +
175A LEU 3.4 1.7 + - - +
176A VAL 3.3 0.2 - - - -
177A ALA* 1.3 77.7 - - + +
179A ILE* 1.3 58.8 + - - +
181A GLY* 3.0 10.8 + - - -
182A LEU 3.1 2.6 + - - -
295A ALA* 3.3 22.2 - - - +
312A GLU* 3.8 6.5 + - - +
313A HIS* 2.6 62.2 + - - +
314A VAL 3.1 10.8 - - - +
318A THR* 3.4 27.0 + - + +
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Residues in contact with ILE 179 (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 LEU* 4.7 0.4 - - + -
176A VAL* 2.7 43.7 + - + +
178A GLN* 1.3 78.4 - - - +
180A PHE* 1.3 68.9 + - - +
182A LEU* 3.1 17.9 + - + +
183A ARG* 3.5 26.1 + - + +
314A VAL* 3.1 52.7 - - + +
319A ALA* 5.4 0.7 - - + -
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Residues in contact with PHE 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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176A VAL* 2.8 20.6 + - + +
179A ILE* 1.3 77.4 - - - +
181A GLY* 1.3 59.0 + - - +
183A ARG* 3.0 21.6 + - + +
184A ASN* 2.8 44.4 + - + -
197A GLY* 3.4 27.1 - - - -
198A LEU* 3.1 40.8 - - + -
201A VAL* 3.7 27.8 - - + -
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Residues in contact with GLY 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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41A SER* 6.0 1.3 - - - -
177A ALA 2.8 15.5 + - - -
178A GLN* 3.0 7.1 + - - -
180A PHE* 1.3 79.3 - - - +
182A LEU* 1.3 52.5 + - - +
184A ASN* 3.1 7.0 + - - +
185A LEU* 2.6 38.8 + - - +
194A ILE* 4.4 14.8 - - - +
198A LEU* 5.3 1.1 - - - -
313A HIS* 5.1 6.5 - - - -
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Residues in contact with LEU 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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178A GLN 3.1 4.9 + - - -
179A ILE* 3.1 12.7 + - + +
181A GLY* 1.3 76.7 - - - +
183A ARG* 1.3 65.0 + - + +
185A LEU* 3.9 7.6 - - + +
186A LEU* 3.0 54.1 + - + +
309A VAL* 4.8 15.0 - - + +
310A PRO* 5.6 0.7 - - + -
313A HIS* 3.1 24.8 + - + +
314A VAL 3.4 14.4 - - - +
315A GLN* 3.8 36.1 - - + +
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Residues in contact with ARG 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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179A ILE* 3.5 25.7 + - + +
180A PHE* 3.0 25.1 + - + +
182A LEU* 1.3 84.9 - - + +
184A ASN* 1.3 56.8 + - - +
186A LEU* 3.3 9.5 + - + +
187A ALA* 2.9 32.0 + - - +
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Residues in contact with ASN 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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180A PHE* 2.8 29.6 + - + +
181A GLY 3.6 3.6 - - - +
183A ARG* 1.3 72.9 - - - +
185A LEU* 1.3 62.1 + - - +
187A ALA* 4.5 2.2 - - - +
188A ASN* 2.7 55.7 + - - +
190A ASP* 4.7 0.7 - - - +
193A PRO 5.1 0.8 + - - -
194A ILE* 3.5 46.6 + - + +
197A GLY* 3.6 21.8 - - - +
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Residues in contact with LEU 185 (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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45A LEU* 5.3 12.8 - - + -
181A GLY 2.6 21.5 + - - +
182A LEU* 3.9 8.7 - - + +
184A ASN* 1.3 74.2 - - - +
186A LEU* 1.3 70.6 + - + +
188A ASN 2.5 21.9 - - - +
189A VAL* 4.0 11.6 + - - +
191A GLY* 4.0 26.9 - - - -
194A ILE* 4.1 15.5 - - + +
309A VAL* 5.4 12.6 - - + -
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Residues in contact with LEU 186 (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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182A LEU* 3.0 49.9 + - + +
183A ARG* 3.6 7.4 - - + +
185A LEU* 1.3 87.7 - - + +
187A ALA* 1.3 63.9 - - - +
188A ASN 4.3 0.9 - - - -
189A VAL* 4.7 4.0 + - - +
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Residues in contact with ALA 187 (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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183A ARG 2.9 17.8 + - - +
184A ASN* 4.1 2.0 - - - +
186A LEU* 1.3 78.2 - - - +
188A ASN* 1.3 72.2 + - - +
189A VAL* 3.8 4.9 + - - +
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Residues in contact with ASN 188 (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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184A ASN* 2.7 48.0 + - - +
185A LEU* 2.5 23.6 - - - +
187A ALA* 1.3 82.2 - - - +
189A VAL* 1.3 63.3 + - - +
190A ASP* 3.4 20.6 + - - +
197A GLY* 5.9 0.2 - - - -
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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