Contacts of the helix formed by residues 184 - 199 (chain Y) in PDB entry 5G04
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 GLN 184 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156Y ILE* 5.5 3.2 - - - +
179Y TYR* 3.0 27.5 + - + +
180Y LYS* 5.6 0.7 - - - -
182Y ALA* 3.6 34.6 - - + +
183Y GLY* 1.3 76.4 - - - +
185Y GLU* 1.3 62.8 + - - +
186Y ARG 3.5 2.0 - - - -
187Y PRO* 3.5 19.2 - - + +
188Y SER* 3.0 27.0 + - - -
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Residues in contact with GLU 185 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180Y LYS* 6.3 0.2 - - - +
183Y GLY* 3.6 10.8 + - - +
184Y GLN* 1.3 71.9 - - - +
186Y ARG* 1.3 57.9 + - - +
187Y PRO* 4.2 0.2 - - - +
188Y SER* 3.4 2.8 + - - -
189Y VAL* 3.0 30.4 + - - +
211Y SER 4.8 2.4 - - - +
212Y LEU* 3.9 49.3 - - + +
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Residues in contact with ARG 186 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185Y GLU* 1.3 75.7 - - + +
187Y PRO* 1.4 68.8 - - + +
189Y VAL* 3.0 28.3 - - + +
190Y THR* 3.4 10.4 + - - +
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Residues in contact with PRO 187 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179Y TYR* 3.6 39.9 - - + -
184Y GLN* 3.5 26.9 - - + +
186Y ARG* 1.4 91.6 - - + +
188Y SER* 1.3 62.6 + - - +
190Y THR* 3.3 22.6 - - + +
191Y SER* 3.3 14.7 + - - -
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Residues in contact with SER 188 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176Y ALA* 3.4 8.6 + - - +
179Y TYR* 3.2 6.3 - - - +
180Y LYS* 3.0 42.0 + - - +
184Y GLN 3.0 11.9 + - - -
185Y GLU* 3.5 8.5 - - - -
186Y ARG 3.3 0.2 - - - -
187Y PRO* 1.3 76.0 - - - +
189Y VAL* 1.3 64.5 + - - +
191Y SER* 3.4 3.5 + - - -
192Y TYR* 3.0 31.0 + - - -
212Y LEU* 3.8 17.3 - - - -
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Residues in contact with VAL 189 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185Y GLU 3.0 11.6 + - - +
186Y ARG* 3.0 39.7 - - + +
188Y SER* 1.3 75.5 - - - +
190Y THR* 1.3 58.5 + - - +
192Y TYR* 3.2 4.0 + - - +
193Y LYS* 2.9 28.7 + - + +
209Y LEU* 3.6 24.3 - - + +
212Y LEU* 3.8 8.4 - - + +
213Y SER 5.7 3.4 - - - +
214Y VAL* 6.1 5.8 - - + -
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Residues in contact with THR 190 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186Y ARG 3.5 11.7 - - - +
187Y PRO* 3.3 18.4 - - + +
189Y VAL* 1.3 81.8 - - - +
191Y SER* 1.3 61.4 + - - +
193Y LYS* 3.3 10.1 + - - +
194Y GLU* 2.9 52.9 + - - +
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Residues in contact with SER 191 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167Y ARG* 4.8 1.0 + - - -
172Y ASN* 3.6 9.9 + - - +
175Y LEU* 3.8 26.0 - - - +
176Y ALA* 3.6 25.3 - - - -
179Y TYR* 4.5 1.4 - - - -
187Y PRO 3.3 15.3 + - - -
188Y SER 3.7 0.7 - - - -
189Y VAL 3.3 0.6 - - - -
190Y THR* 1.3 82.7 - - - +
192Y TYR* 1.3 56.5 + - - +
194Y GLU* 3.2 17.4 + - - +
195Y VAL* 2.9 32.0 + - - +
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Residues in contact with TYR 192 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173Y MET* 4.8 10.3 - - + -
176Y ALA* 3.5 23.4 - - + +
177Y ASN* 2.8 26.0 + - - -
180Y LYS* 3.2 36.4 + - + -
188Y SER* 3.0 22.3 + - - +
189Y VAL 3.2 0.2 + - - -
191Y SER* 1.3 71.3 - - - +
193Y LYS* 1.3 61.3 + - - +
195Y VAL* 3.2 10.5 - - + +
196Y LEU* 2.9 34.6 + - - +
204Y ASP 4.4 2.9 + - - -
205Y ALA* 3.6 35.4 - - + +
208Y GLY* 4.0 10.4 - - - -
209Y LEU* 3.4 26.9 - - + -
212Y LEU* 3.7 18.6 - - + -
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Residues in contact with LYS 193 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Y VAL* 2.9 15.1 + - + +
190Y THR* 3.4 13.7 - - - +
192Y TYR* 1.3 75.5 - - - +
194Y GLU* 1.3 57.4 + - + +
196Y LEU* 3.3 15.9 + - + +
197Y ARG* 2.9 44.2 + - - +
209Y LEU* 4.8 4.1 - - + +
221Y SER* 3.9 26.9 + - - -
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Residues in contact with GLU 194 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164Y SER* 4.5 18.1 - - - +
167Y ARG* 4.3 15.3 + - - -
172Y ASN* 3.7 28.1 + - - +
190Y THR* 2.9 44.1 + - - +
191Y SER* 3.2 14.5 + - - +
193Y LYS* 1.3 78.1 - - + +
195Y VAL* 1.3 59.9 + - - +
197Y ARG* 3.1 35.1 - - - +
198Y GLN* 3.4 9.2 + - - +
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Residues in contact with VAL 195 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49X LEU* 5.3 6.1 - - + -
52X ASN* 5.6 0.4 - - - +
169Y PRO* 3.1 34.0 - - + +
172Y ASN* 3.4 12.1 - - + -
173Y MET* 3.4 23.3 - - + +
191Y SER 2.9 17.2 + - - +
192Y TYR* 3.2 25.4 - - + +
194Y GLU* 1.3 72.3 - - - +
196Y LEU* 1.3 62.3 + - - +
198Y GLN* 3.5 7.0 - - - +
199Y CYS* 3.3 29.3 + - - -
200Y PRO 4.3 0.2 - - - +
202Y ALA* 5.1 1.3 - - + +
205Y ALA* 3.6 25.1 - - + -
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Residues in contact with LEU 196 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192Y TYR 2.9 18.4 + - - +
193Y LYS* 3.7 15.7 - - - +
195Y VAL* 1.3 75.2 - - - +
197Y ARG* 1.3 63.5 + - - +
198Y GLN 3.1 1.6 - - - -
200Y PRO* 2.9 54.3 - - + +
202Y ALA 3.8 4.3 - - - +
205Y ALA* 3.7 24.5 - - + -
206Y ILE* 3.8 22.7 - - + -
209Y LEU* 3.8 26.5 - - + -
218Y GLU* 5.7 1.1 - - + +
221Y SER* 4.6 10.8 - - - +
222Y MET* 4.1 18.4 - - + -
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Residues in contact with ARG 197 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193Y LYS* 2.9 27.6 + - - +
194Y GLU* 3.1 40.3 - - - +
196Y LEU* 1.3 76.2 - - - +
198Y GLN* 1.3 60.2 + - - +
199Y CYS 5.3 0.5 - - - -
200Y PRO* 5.7 0.5 - - - +
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Residues in contact with GLN 198 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X ALA* 5.0 4.3 - - - +
169Y PRO* 3.2 47.2 - - + +
172Y ASN* 6.3 0.2 - - - +
194Y GLU 3.4 13.4 + - - +
195Y VAL 3.5 11.4 - - - +
196Y LEU 3.1 0.4 - - - -
197Y ARG* 1.3 80.5 - - - +
199Y CYS* 1.3 69.5 + - - +
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Residues in contact with CYS 199 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X HIS* 4.5 6.4 + - - -
43X ASP* 6.6 0.2 - - + -
44X MET* 4.9 11.2 - - + -
47X ALA* 6.2 1.6 - - - -
49X LEU* 5.4 7.4 - - - -
169Y PRO* 5.4 3.8 - - - -
195Y VAL* 3.3 15.0 + - - -
196Y LEU 3.3 2.6 + - - -
197Y ARG 5.3 0.2 - - - -
198Y GLN* 1.3 90.4 - - - +
200Y PRO* 1.3 79.8 - - - +
201Y LEU* 3.5 28.6 - - + +
202Y ALA* 4.3 10.5 - - - -
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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