Contacts of the helix formed by residues 177 - 193 (chain A) in PDB entry 2Y0N
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 PRO 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A GLU 3.6 8.7 - - - +
176A ILE* 1.3 86.1 - - + +
178A GLU* 1.3 56.0 + - - +
179A VAL* 3.1 3.6 - - + +
180A LEU* 2.7 30.7 + - + -
181A LYS 2.9 9.4 + - - -
488A LEU* 3.8 36.8 - - + +
489A ARG* 3.8 39.3 - - - +
492A ALA* 3.9 17.5 - - + -
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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
----------------------------------------------------------
176A ILE 3.3 3.7 + - - +
177A PRO* 1.3 71.0 - - - +
179A VAL* 1.3 61.7 + - - +
181A LYS* 3.5 31.4 + - + +
182A LYS* 3.0 39.3 + - - +
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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 PRO* 5.1 1.6 - - + -
178A GLU* 1.3 78.7 - - + +
180A LEU* 1.3 58.6 + - - +
182A LYS* 3.7 19.3 - - + +
183A GLN* 3.3 21.7 + - - +
489A ARG* 6.3 0.4 - - - +
492A ALA* 4.5 24.0 - - + +
495A HIS* 4.1 36.9 + - + +
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Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ILE* 3.8 9.2 - - + -
177A PRO* 2.7 25.4 + - + +
179A VAL* 1.3 73.1 - - - +
181A LYS* 1.3 58.5 + - - +
182A LYS 3.3 0.4 - - - -
183A GLN* 3.3 5.9 + - + +
184A LEU* 2.9 32.4 + - - +
457A LEU* 3.8 16.2 - - + +
488A LEU* 3.4 48.5 - - + +
491A LEU* 3.8 26.7 - - + +
492A ALA* 3.9 13.0 - - + +
495A HIS* 4.6 8.1 - - + -
499A PHE* 4.0 19.3 - - + -
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Residues in contact with LYS 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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176A ILE* 3.5 40.8 - - + +
177A PRO 2.9 5.1 + - - -
178A GLU* 3.5 32.6 + - + +
180A LEU* 1.3 74.4 - - - +
182A LYS* 1.3 65.8 + - + +
184A LEU* 3.2 6.5 + - - +
185A GLU* 3.2 28.8 + - - +
593E TRP* 3.8 42.9 - - + +
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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
----------------------------------------------------------
178A GLU* 3.0 30.9 + - + +
179A VAL* 3.7 18.6 - - + +
181A LYS* 1.3 72.9 - - + +
183A GLN* 1.3 57.8 + - - +
185A GLU* 2.8 38.0 + - - +
186A ASP* 2.8 21.8 + - - +
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Residues in contact with GLN 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 VAL 3.3 12.5 + - - +
180A LEU* 3.3 13.0 + - - +
182A LYS* 1.3 78.1 - - - +
184A LEU* 1.3 57.1 + - - +
186A ASP* 3.3 15.7 + - - +
187A ASP* 2.9 29.3 + - - +
190A TYR* 5.8 1.6 - - - -
454A GLN* 5.0 1.0 - - - +
457A LEU* 4.0 8.1 - - + -
495A HIS* 3.3 23.3 + - + +
499A PHE* 3.5 48.8 - - + +
501A GLU* 5.4 4.0 - - - +
504A TYR* 4.0 22.4 + - - -
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Residues in contact with LEU 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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176A ILE* 4.0 18.8 - - + -
180A LEU 2.9 16.7 + - - +
181A LYS 3.5 8.1 - - - +
182A LYS 3.1 0.4 - - - -
183A GLN* 1.3 72.8 - - - +
185A GLU* 1.3 60.0 + - - +
187A ASP* 3.4 9.9 - - + +
188A CYS* 3.1 26.5 + - - +
275A TYR* 5.1 0.2 + - - -
454A GLN 5.1 0.7 - - - +
457A LEU* 3.8 29.4 - - + +
458A ARG* 4.1 33.0 - - + +
461A VAL* 3.8 24.2 - - + -
589E PHE* 4.7 4.0 - - + -
591E LEU* 3.7 25.2 - - + +
593E TRP* 4.4 4.0 - - + -
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Residues in contact with GLU 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 LYS* 3.2 15.6 + - - +
182A LYS* 2.8 23.0 + - - +
184A LEU* 1.3 69.6 - - - +
186A ASP* 1.3 64.4 + - - +
188A CYS* 3.3 7.6 + - - +
189A TYR* 3.1 22.4 + - - +
591E LEU* 4.8 7.0 - - + -
593E TRP* 2.8 35.7 + - + +
594E LEU 5.8 2.9 - - - +
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Residues in contact with ASP 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* 2.8 24.2 + - - +
183A GLN* 3.4 23.0 - - - +
185A GLU* 1.3 71.8 - - - +
187A ASP* 1.3 64.6 + - - +
189A TYR* 3.1 9.5 + - - +
190A TYR* 3.0 44.1 + - + -
501A GLU* 5.6 2.8 - - - +
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Residues in contact with ASP 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 GLN* 2.9 24.2 + - - +
184A LEU* 3.4 13.0 - - + +
186A ASP* 1.3 74.2 - - - +
188A CYS* 1.3 63.9 + - - +
190A TYR* 3.3 13.7 + - - +
191A ILE* 3.4 19.8 + - - +
198A VAL* 5.0 0.2 - - - +
275A TYR* 4.9 0.5 - - - -
454A GLN* 4.0 14.1 - - - +
458A ARG* 2.5 39.3 + - - +
504A TYR* 2.6 38.7 + - - +
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Residues in contact with CYS 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 LEU 3.1 10.0 + - - +
185A GLU* 3.5 9.4 - - - +
186A ASP 3.2 0.2 - - - -
187A ASP* 1.3 79.8 - - - +
189A TYR* 1.3 65.1 + - - +
191A ILE* 3.0 12.1 + - - -
192A ASN* 2.9 33.9 + - - +
193A ARG* 6.3 0.9 - - - -
275A TYR* 3.4 36.6 - - - +
591E LEU* 3.8 13.0 - - + -
594E LEU 6.0 1.3 - - - -
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Residues in contact with TYR 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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185A GLU 3.1 8.8 + - - +
186A ASP* 3.1 13.1 + - - +
188A CYS* 1.3 77.6 - - - +
190A TYR* 1.3 65.7 + + - +
192A ASN* 4.6 0.4 - - - -
193A ARG* 3.2 45.7 + - + +
194A ARG* 3.0 69.1 + - + +
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Residues in contact with TYR 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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183A GLN* 5.8 1.8 - - - -
186A ASP* 3.0 44.0 + - + -
187A ASP* 3.5 11.4 - - - +
188A CYS 3.1 0.2 + - - -
189A TYR* 1.3 78.6 - + + +
191A ILE* 1.3 52.6 + - - +
194A ARG* 3.4 34.5 + - - -
195A LYS 3.2 9.4 + - - -
196A ARG* 2.7 59.7 + - + +
501A GLU* 2.8 40.3 + - + +
504A TYR* 3.9 42.4 - + + -
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Residues in contact with ILE 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 ASP* 3.4 33.0 - - - +
188A CYS 3.0 4.6 + - - +
190A TYR* 1.3 79.9 - - - +
192A ASN* 1.3 59.8 + - - +
193A ARG 3.5 0.4 - - - -
195A LYS* 3.5 18.2 - - - +
196A ARG 3.3 23.0 + - - +
197A LEU* 4.6 3.5 - - + +
198A VAL* 5.1 4.3 - - + +
275A TYR* 4.2 18.4 - - + -
277A TYR* 4.3 19.4 - - + +
278A GLU* 3.4 43.1 - - + +
458A ARG* 3.5 12.3 - - - +
504A TYR* 4.3 11.9 - - + -
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Residues in contact with ASN 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 CYS* 2.9 31.4 + - - +
189A TYR* 4.4 0.5 + - - -
191A ILE* 1.3 74.5 - - + +
193A ARG* 1.3 70.1 + - - +
195A LYS* 4.7 5.3 - - - +
275A TYR* 3.1 48.7 - - - +
276A PRO* 5.6 0.8 - - + +
277A TYR* 3.9 34.7 + - + -
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Residues in contact with ARG 193 (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 CYS* 6.3 0.8 - - - -
189A TYR* 3.2 49.9 + - + +
191A ILE 3.5 0.8 - - - -
192A ASN* 1.3 90.2 + - - +
194A ARG* 1.3 60.5 + - - +
195A LYS* 3.0 13.8 + - - +
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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