Contacts of the helix formed by residues 181 - 187 (chain K) in PDB entry 5GJQ
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 VAL 181 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177K VAL* 2.6 20.4 + - + +
180K ALA* 1.3 87.6 - - + +
182K GLU* 1.3 59.2 + - - +
183K LEU 3.1 1.8 - - - -
184K PRO* 3.6 0.7 - - - -
185K LEU* 2.4 66.7 + - + +
202K VAL* 5.3 5.2 - - + -
219K VAL* 5.3 1.8 - - + -
261K ILE* 3.7 22.2 - - + -
306K LYS* 3.8 27.1 - - + -
307K VAL 5.7 0.2 - - - +
308K ILE* 4.4 19.1 - - + -
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Residues in contact with GLU 182 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K TYR* 3.6 19.1 + - - -
177K VAL* 3.6 3.1 + - + +
178K ARG* 3.2 49.7 + - + +
181K VAL* 1.3 82.5 - - - +
183K LEU* 1.3 61.4 + - + +
185K LEU* 3.9 2.7 - - - +
186K THR* 3.1 31.4 + - + +
219K VAL* 6.0 6.7 - - + +
222K HIS* 5.8 5.3 - - - +
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Residues in contact with LEU 183 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368J MET* 6.2 1.1 - - - -
371J LEU* 4.8 14.4 - - + -
372J ARG* 4.7 20.2 - - + -
374J ARG* 2.9 40.8 - - - +
178K ARG* 2.7 29.7 + - + +
179K GLU* 4.7 14.1 - - + +
182K GLU* 1.3 74.6 - - + +
184K PRO* 1.3 74.9 - - + +
185K LEU 3.1 1.3 - - - -
186K THR* 2.7 20.9 + - - +
187K HIS* 2.9 25.7 + - + +
191K TYR* 4.6 5.8 - - + +
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Residues in contact with PRO 184 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178K ARG 2.9 8.5 - - - +
179K GLU 2.3 24.7 - - - +
180K ALA* 3.1 18.4 - - - +
181K VAL 3.4 4.9 - - - +
183K LEU* 1.3 94.0 - - + +
185K LEU* 1.3 59.8 + - - +
187K HIS 3.4 12.8 - - - +
188K PHE* 4.4 9.0 - - - -
191K TYR* 2.0 56.2 - - + +
198K PRO* 4.4 7.2 - - + +
199K PRO* 4.9 0.9 - - + -
306K LYS* 4.4 7.4 + - - +
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Residues in contact with LEU 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181K VAL* 2.4 50.5 + - + +
182K GLU* 3.9 4.7 - - - +
184K PRO* 1.3 71.2 - - - +
186K THR* 1.3 63.3 + - + +
188K PHE* 4.7 1.0 - - - -
223K THR* 5.8 0.7 - - - +
224K THR* 5.8 1.8 - - - +
225K ALA* 4.3 6.7 - - + -
259K PRO* 3.2 48.3 - - + +
260K ALA 4.9 0.7 - - - -
261K ILE* 4.1 15.5 - - + -
304K ASN* 3.4 35.3 + - + +
306K LYS* 3.7 27.7 - - + +
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Residues in contact with THR 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K GLU* 3.1 18.0 + - + +
183K LEU* 2.7 16.7 + - - +
185K LEU* 1.3 82.1 - - + +
187K HIS* 1.3 79.2 + - - +
188K PHE* 3.1 10.2 + - - +
224K THR* 4.9 15.0 - - + +
304K ASN* 5.5 0.2 + - - -
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Residues in contact with HIS 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371J LEU* 5.4 1.1 - - + -
374J ARG* 3.4 36.9 + - + +
183K LEU* 2.9 17.7 + - + +
184K PRO 3.4 3.0 - - - +
186K THR* 1.3 82.4 + - - +
188K PHE* 1.3 61.0 + - - +
189K GLU* 3.5 2.9 + - - +
190K LEU* 4.3 20.4 + - + +
191K TYR* 2.9 28.9 + - + -
226Q LYS* 5.6 2.6 + - - -
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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