Contacts of the helix formed by residues 177 - 188 (chain A) in PDB entry 4OTZ
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 ALA 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A VAL* 3.0 15.7 + - - +
176A VAL* 1.3 79.2 - - + +
178A PRO* 1.4 69.8 - - + +
179A ASN 3.1 0.5 + - - -
180A SER* 2.9 23.7 + - - -
181A VAL 3.8 0.9 + - - -
208A GLU* 4.4 14.4 - - + +
211A ILE* 4.0 11.4 - - + -
212A PHE* 3.4 36.5 - - + -
301A ALA* 4.8 1.8 - - - -
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Residues in contact with PRO 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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173A VAL 3.7 2.0 - - - +
174A SER 3.5 26.5 - - - +
175A VAL* 4.1 3.6 - - - +
176A VAL 3.5 4.7 - - - +
177A ALA* 1.4 93.8 - - + +
179A ASN* 1.3 62.4 + - - +
181A VAL* 3.1 15.0 + - + +
182A LYS* 3.1 31.1 + - - +
211A ILE* 3.9 6.7 - - + -
212A PHE* 5.5 0.2 - - + -
215A THR* 3.6 34.0 - - + +
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Residues in contact with ASN 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 VAL 4.4 9.4 + - - -
176A VAL 3.6 9.3 + - - +
177A ALA 3.1 1.4 + - - -
178A PRO* 1.3 79.2 - - - +
180A SER* 1.3 57.2 + - - +
182A LYS* 3.3 21.4 + - - +
183A ALA* 2.9 28.4 + - - +
396A PHE* 3.7 34.2 + - - +
397A TYR* 4.7 2.6 - - - +
398A VAL* 3.6 17.6 - - + +
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Residues in contact with SER 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A VAL 4.4 1.0 + - - -
177A ALA 2.9 18.7 + - - -
179A ASN* 1.3 75.4 - - - +
181A VAL* 1.3 60.9 + - - +
183A ALA* 3.4 3.9 + - - +
184A ALA* 3.0 22.5 + - - +
212A PHE* 3.4 6.8 - - - -
277A ILE* 3.4 39.4 - - - +
278A GLY 5.1 0.2 + - - -
299A LEU* 4.3 4.9 - - - +
301A ALA* 4.0 26.5 + - - +
398A VAL* 3.9 14.5 - - - +
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Residues in contact with VAL 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A ALA 4.3 0.9 - - - +
178A PRO 3.1 8.0 + - - +
180A SER* 1.3 74.3 - - - +
182A LYS* 1.3 65.5 + - - +
184A ALA* 3.2 4.2 + - - +
185A LEU* 3.1 35.8 + - + +
212A PHE* 3.7 31.9 - - + +
215A THR* 3.8 28.0 - - + -
216A VAL* 4.9 5.6 - - + +
219A GLN* 4.4 5.6 - - + -
221A LEU* 4.6 12.8 - - + -
250A LEU* 4.7 9.0 - - + -
252A ILE* 4.2 7.4 - - + -
277A ILE* 3.6 14.8 - - + -
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Residues in contact with LYS 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 PRO* 3.1 29.6 + - - +
179A ASN* 3.3 23.2 + - - +
181A VAL* 1.3 76.9 - - + +
183A ALA* 1.3 56.6 + - - +
185A LEU* 3.3 10.3 + - - +
186A LYS* 3.0 27.3 + - - +
215A THR* 5.2 2.5 - - + -
219A GLN* 4.0 29.4 - - - +
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Residues in contact with ALA 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 ASN 2.9 17.4 + - - +
180A SER 3.6 5.8 - - - +
181A VAL 3.2 0.2 - - - -
182A LYS* 1.3 73.3 - - - +
184A ALA* 1.3 64.2 + - - +
186A LYS* 3.2 10.3 + - - +
187A GLN* 3.1 27.4 + - - +
299A LEU* 4.3 4.7 - - + -
398A VAL* 3.9 26.5 - - + -
415A LEU* 3.9 16.8 - - + +
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Residues in contact with ALA 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 SER 3.0 14.4 + - - +
181A VAL 3.2 8.0 + - - +
183A ALA* 1.3 75.2 - - - +
185A LEU* 1.3 57.8 + - + +
187A GLN* 3.3 5.6 + - - +
188A ASN* 2.9 24.1 + - - +
191A ILE* 3.6 17.1 - - + +
250A LEU* 4.1 17.7 - - + -
275A ALA* 5.0 2.7 - - + -
277A ILE* 4.0 13.7 - - + -
299A LEU* 3.7 19.9 - - + +
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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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181A VAL* 3.1 18.8 + - + +
182A LYS* 3.7 10.1 - - - +
183A ALA 3.2 0.4 - - - -
184A ALA* 1.3 75.5 - - + +
186A LYS* 1.3 66.2 + - - +
188A ASN 3.8 5.4 - - - +
189A PRO* 3.1 34.6 - - + +
191A ILE* 3.8 31.9 - - + +
219A GLN* 3.8 42.4 - - + +
221A LEU* 4.1 23.8 - - + -
250A LEU* 6.0 0.9 - - + -
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Residues in contact with LYS 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 LYS 3.0 12.3 + - - +
183A ALA* 3.2 12.5 + - - +
185A LEU* 1.3 80.3 - - - +
187A GLN* 1.3 63.9 + - + +
189A PRO* 3.8 10.9 - - - +
415A LEU* 6.6 0.4 - - + -
416A LYS* 4.3 15.8 + - - -
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Residues in contact with GLN 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 ALA 3.1 13.8 + - - +
184A ALA* 3.8 6.7 - - - +
186A LYS* 1.3 80.3 - - + +
188A ASN* 1.3 60.8 + - + +
189A PRO* 3.9 4.0 - - - +
299A LEU* 4.2 11.4 - - - +
400A GLN* 2.9 42.1 + - - -
415A LEU* 3.8 25.0 - - + +
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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 ALA 2.9 10.6 + - - +
185A LEU* 3.2 7.6 - - - +
187A GLN* 1.3 81.5 - - + +
189A PRO* 1.3 61.1 - - - +
190A ASN* 3.0 30.9 + - - +
191A ILE* 3.2 40.8 + - + +
249A ASP* 5.2 6.7 + - - +
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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