Contacts of the helix formed by residues 186 - 196 (chain B) in PDB entry 5GGP
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 LYS 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155B HIS* 5.2 1.6 - - - -
157B ASP* 2.7 46.0 + - - +
158B GLU* 2.9 26.2 + - - +
184B HIS* 4.1 9.0 - - + +
185B LEU* 1.3 74.3 - - - +
187B ASP* 1.3 58.4 + - - +
188B THR* 3.2 5.1 + - - +
189B ALA 3.2 2.8 + - - +
190B LYS* 2.7 32.3 + - - +
301B NA 3.3 19.0 - - - -
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Residues in contact with ASP 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B LYS* 1.3 76.1 - - - +
188B THR* 1.3 57.8 + - - +
190B LYS* 3.9 19.7 + - - +
191B ALA* 2.9 32.9 + - - +
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Residues in contact with THR 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B VAL* 4.8 17.3 - - + -
186B LYS* 3.3 2.8 - - - +
187B ASP* 1.3 78.9 - - - +
189B ALA* 1.3 58.8 + - - +
191B ALA* 3.8 3.4 - - - +
192B LEU* 3.0 31.2 + - + +
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Residues in contact with ALA 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ASP* 3.7 32.9 + - + +
160B MET* 4.0 6.8 - - + +
161B VAL* 3.6 26.9 - - + +
185B LEU* 3.8 11.7 - - + -
186B LYS 3.2 5.1 + - - +
188B THR* 1.3 76.9 - - - +
190B LYS* 1.3 67.2 + - - +
191B ALA 3.3 0.3 + - - -
192B LEU* 3.4 10.5 + - - +
193B LEU* 3.6 17.7 - - - +
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Residues in contact with LYS 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B SER* 5.1 4.7 + - - -
185B LEU* 3.4 39.1 + - + +
186B LYS 2.7 21.4 + - - +
187B ASP* 3.9 17.2 + - - +
189B ALA* 1.3 74.3 - - - +
191B ALA* 1.3 63.2 + - - +
193B LEU* 3.8 3.7 - - - +
194B ARG* 6.2 0.2 - - - +
201B GLY 3.5 11.1 - - - +
202B PRO* 3.5 16.9 - - + +
203B ALA* 4.0 25.4 - - - +
204B LEU 3.8 18.6 + - - +
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Residues in contact with ALA 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B ASP 2.9 19.1 + - - +
188B THR* 3.8 3.6 - - - +
190B LYS* 1.3 75.1 - - - +
192B LEU* 1.3 52.0 + - - +
193B LEU 2.8 5.1 + - - -
194B ARG* 2.4 67.5 + - - +
195B SER 3.6 1.4 + - - -
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Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B MET* 6.3 0.7 - - + -
161B VAL* 4.1 39.9 - - + +
164B LEU* 4.3 22.0 - - + -
165B ASN* 5.4 1.3 - - - +
188B THR* 3.0 19.4 + - + +
189B ALA 3.4 6.4 + - - +
191B ALA* 1.3 73.5 - - - +
193B LEU* 1.3 62.7 + - + +
195B SER* 3.2 26.1 + - - +
196B LEU* 3.3 25.4 + - + +
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Residues in contact with LEU 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B ILE* 5.0 3.8 - - + -
160B MET* 4.7 16.6 - - + -
164B LEU* 4.3 15.7 - - + -
175B CYS* 5.5 4.7 - - - -
185B LEU* 4.8 9.2 - - + -
189B ALA 3.6 17.0 - - - +
190B LYS 3.8 1.8 - - - +
191B ALA 2.8 3.6 + - - -
192B LEU* 1.3 74.8 - - + +
194B ARG* 1.3 60.9 + - - +
196B LEU* 3.0 33.5 + - + +
198B SER* 3.1 22.7 + - - -
201B GLY* 3.8 26.5 - - - +
202B PRO* 3.8 17.0 - - + -
204B LEU* 5.7 0.7 - - + -
210B TRP* 4.1 23.3 - - + -
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Residues in contact with ARG 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B LYS* 6.2 0.2 - - - +
191B ALA* 2.4 52.7 + - - +
193B LEU* 1.3 69.6 - - - +
195B SER* 1.3 59.7 + - - +
197B GLY* 3.1 14.9 + - - -
198B SER 3.3 13.0 - - - +
199B GLN* 5.9 0.7 - - - -
202B PRO* 3.4 35.8 - - + +
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Residues in contact with SER 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B ALA 3.6 2.0 + - - -
192B LEU* 3.2 24.7 + - - +
194B ARG* 1.3 78.2 - - - +
196B LEU* 1.3 61.1 + - - +
197B GLY 3.2 1.6 + - - -
217B GLY* 5.5 5.7 + - - -
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B LEU* 4.2 17.0 - - + -
173B LEU* 3.9 24.0 - - + -
175B CYS* 6.1 2.9 - - - -
192B LEU* 3.4 24.0 - - + +
193B LEU* 3.0 32.8 + - + +
195B SER* 1.3 81.1 - - - +
197B GLY* 1.3 56.4 + - - +
198B SER* 3.5 2.2 - - - +
212B PHE* 3.7 20.3 - - + -
215B ARG 4.3 13.5 - - - +
216B LYS* 3.9 36.8 - - + -
217B GLY 4.8 3.4 - - - +
218B GLY* 4.7 5.7 + - - -
220B VAL* 4.2 3.1 - - - +
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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