Contacts of the helix formed by residues 177 - 192 (chain A) in PDB entry 6ABP
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 ASN 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A LYS* 4.8 5.1 - - - +
11A GLN* 3.5 27.0 + - - +
14A GLU* 4.4 7.1 - - - +
142A ALA* 3.3 25.8 - - - +
145A LEU* 3.9 17.2 - - - +
174A THR* 4.0 5.7 - - - +
176A SER* 1.3 75.3 - - - +
178A ASP* 1.3 58.0 + - - +
204A MET* 3.6 32.4 - - + +
205A ASN* 4.6 3.1 + - - +
207A SER* 4.4 3.7 - - - -
208A THR* 4.5 13.6 + - - +
307A ARA 5.4 0.7 - - - +
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Residues in contact with ASP 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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11A GLN* 4.9 7.2 - - - +
13A GLU* 5.9 0.9 - - - +
176A SER* 2.4 35.2 + - - +
177A ASN* 1.3 74.6 - - - +
179A ILE* 1.3 60.7 + - - +
180A PRO* 3.6 16.4 - - + +
181A GLY 3.0 8.7 + - - -
182A ALA* 3.0 30.3 + - - +
207A SER* 3.8 17.5 - - - +
208A THR* 4.5 1.1 + - - -
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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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178A ASP* 1.3 70.0 - - - +
180A PRO* 1.3 71.7 - - + +
182A ALA 3.3 0.9 + - - -
183A PHE* 2.9 36.4 + - + +
207A SER* 3.5 31.2 - - - +
210A LEU* 4.1 26.0 - - + -
211A GLY* 3.6 13.8 - - - -
214A ARG* 4.7 15.5 - - + +
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Residues in contact with PRO 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 SER* 5.2 0.4 - - - +
178A ASP* 3.6 18.2 - - + +
179A ILE* 1.3 98.4 - - + +
181A GLY* 1.3 60.3 + - - +
183A PHE* 3.6 6.3 - - + +
184A ASP* 3.2 31.7 + - - +
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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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174A THR* 3.0 17.8 + - - -
175A LYS* 4.6 7.0 + - - -
176A SER* 3.2 22.1 + - - -
178A ASP* 3.0 13.1 + - - -
180A PRO* 1.3 76.7 - - - +
182A ALA* 1.3 63.7 + - - +
184A ASP* 3.5 6.9 + - - +
185A ALA* 3.1 19.6 + - - +
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Residues in contact with ALA 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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140A ILE* 4.1 6.6 - - + +
174A THR* 3.4 8.3 + - + +
178A ASP 3.0 18.9 + - - +
179A ILE 3.8 2.7 - - - +
181A GLY* 1.3 74.7 - - - +
183A PHE* 1.3 55.0 + - - +
185A ALA* 3.4 5.1 + - - +
186A ALA* 2.8 37.6 + - - +
208A THR* 3.2 42.2 - - + +
211A GLY* 3.9 6.5 - - - -
212A GLY 4.1 0.4 - - - +
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Residues in contact with PHE 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* 2.9 22.1 + - + +
180A PRO* 3.6 7.0 - - + +
182A ALA* 1.3 72.4 - - - +
184A ASP* 1.3 76.9 + - - +
186A ALA 3.3 0.2 + - - -
187A ASN* 2.8 48.7 + - + +
211A GLY* 3.5 14.5 - - - +
214A ARG* 3.8 17.3 - - + -
215A ALA* 3.5 37.4 - - + +
218A GLY* 5.9 4.0 - - - -
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Residues in contact with ASP 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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175A LYS* 4.5 11.5 + - - +
180A PRO* 3.2 13.8 + - - +
181A GLY* 3.5 11.0 - - - +
183A PHE* 1.3 96.1 - - - +
185A ALA* 1.3 62.3 + - - +
187A ASN* 3.4 4.6 + - - +
188A SER* 3.2 23.2 + - - -
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Residues in contact with ALA 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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140A ILE* 4.2 3.6 - - + -
172A VAL* 3.6 24.3 - - + +
173A PRO 3.6 23.3 - - - +
174A THR* 4.1 11.4 - - - -
175A LYS* 4.5 6.9 - - - +
181A GLY 3.1 14.4 + - - +
182A ALA 3.6 4.5 - - - +
184A ASP* 1.3 80.0 - - - +
186A ALA* 1.4 64.2 + - - +
188A SER* 3.0 20.7 + - - -
189A MET* 3.3 5.0 + - - +
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Residues in contact with ALA 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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138A MET* 3.5 29.6 - - + +
140A ILE* 4.2 2.2 - - + -
172A VAL* 4.8 1.3 - - - -
182A ALA 2.8 21.4 + - - +
185A ALA* 1.4 74.3 - - - +
187A ASN* 1.3 63.6 + - - +
189A MET* 3.1 2.6 + - - +
190A LEU* 2.8 28.3 + - + +
212A GLY* 3.7 15.9 - - - +
215A ALA* 3.7 18.8 - - + -
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Residues in contact with ASN 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 PHE* 2.8 36.3 + - + +
184A ASP* 3.7 6.7 - - - +
186A ALA* 1.3 77.1 - - - +
188A SER* 1.3 62.4 + - - +
190A LEU* 3.2 12.5 + - - +
191A VAL* 3.4 20.2 + - - +
215A ALA* 3.8 16.3 - - + +
218A GLY* 5.6 0.3 - - - -
219A GLN* 3.2 34.9 + - - +
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Residues in contact with SER 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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172A VAL* 4.0 11.1 - - - +
184A ASP 3.2 13.6 + - - -
185A ALA* 3.0 15.0 + - - -
186A ALA 3.2 0.2 - - - -
187A ASN* 1.3 76.9 - - - +
189A MET* 1.3 61.0 + - - +
191A VAL* 3.4 13.4 - - - +
192A GLN* 3.2 29.5 + - - +
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Residues in contact with MET 189 (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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138A MET* 4.3 22.0 - - + -
170A TYR* 3.8 19.1 - - + -
171A GLN 3.6 25.4 - - - +
172A VAL* 3.9 20.0 - - + -
185A ALA 3.3 7.7 + - - +
186A ALA 3.1 7.2 + - - +
188A SER* 1.3 80.2 + - - +
190A LEU* 1.3 65.8 + - - +
192A GLN* 3.1 27.7 + - - +
193A HIS* 3.4 45.6 - - + +
199A TRP* 4.5 7.0 - - + -
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Residues in contact with LEU 190 (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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138A MET* 4.9 6.7 - - + -
186A ALA* 2.8 22.1 + - + +
187A ASN* 3.2 5.6 + - - +
189A MET* 1.3 77.9 - - - +
191A VAL* 1.3 60.1 + - - +
192A GLN 3.1 0.4 - - - -
193A HIS* 3.2 19.8 + - - +
194A PRO* 4.2 1.7 - - - +
199A TRP* 3.3 44.9 + - + +
215A ALA* 3.6 39.9 - - + +
216A THR* 3.7 18.4 - - + +
219A GLN* 3.8 21.5 - - + -
221A PHE* 4.3 8.9 - - + -
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Residues in contact with VAL 191 (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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187A ASN* 3.4 15.2 + - - +
188A SER* 3.4 18.6 - - - +
190A LEU* 1.3 74.0 - - - +
192A GLN* 1.3 65.2 + - + +
193A HIS 3.3 0.6 + - - -
194A PRO* 3.9 9.1 - - - +
219A GLN* 4.1 28.3 - - - +
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Residues in contact with GLN 192 (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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188A SER* 3.2 29.0 + - - +
189A MET* 3.1 28.9 + - - +
191A VAL* 1.3 81.5 - - + +
193A HIS* 1.3 73.1 + - + +
194A PRO* 3.4 9.3 - - - +
195A GLU* 4.2 1.6 - - - +
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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