Contacts of the helix formed by residues 178 - 185 (chain U) in PDB entry 2GLJ
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 LEU 178 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176U ASP 3.4 2.7 + - - -
177U ILE* 1.3 88.4 - - + +
179U VAL* 1.3 66.1 + - - +
180U HIS* 3.5 35.9 - - + +
181U LEU* 3.1 20.2 + - + +
182U ALA* 3.0 17.0 + - - +
345X ALA* 3.4 34.5 - - + -
346X ALA 6.1 0.4 - - - +
355X MET* 5.5 5.4 - - + -
408X LEU* 4.3 6.3 - - + -
439X ASN* 4.8 3.8 - - - +
440X MSE 3.9 40.8 - - + +
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Residues in contact with VAL 179 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177U ILE 3.7 0.4 + - - -
178U LEU* 1.3 71.8 - - - +
180U HIS* 1.3 86.6 + - + +
181U LEU 3.1 1.0 + - - -
182U ALA* 3.2 19.5 + - - +
183U SER* 4.3 3.5 + - - -
134X GLY 4.1 16.2 - - - +
135X ILE* 3.4 20.4 - - - +
136X LYS* 3.6 17.9 - - + +
137X LYS* 3.3 31.2 - - + +
440X MSE 4.8 3.6 + - - +
441X HIS* 4.4 13.9 - - + +
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Residues in contact with HIS 180 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178U LEU* 3.0 28.2 - - + -
179U VAL* 1.3 86.9 - - + +
181U LEU* 1.3 71.6 + - + +
182U ALA 3.6 0.2 - - - -
183U SER* 5.1 3.8 + - - -
408X LEU* 4.4 11.7 - - + -
414X GLY* 3.0 23.9 - - - -
415X GLY 3.9 13.9 + - - +
440X MSE 3.1 31.9 - - + +
441X HIS* 3.5 26.3 + + - -
6047X MN 4.6 1.6 - - - -
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Residues in contact with LEU 181 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177U ILE* 4.3 6.8 - - + +
178U LEU* 3.1 23.5 + - + -
180U HIS* 1.3 94.3 - - + +
182U ALA* 1.3 58.0 + - - +
183U SER* 3.1 10.0 + - - +
184U GLU* 4.3 4.5 + - - +
345X ALA* 5.6 0.2 - - + -
354X VAL* 3.4 48.2 - - + +
355X MET* 4.1 7.6 - - + -
408X LEU* 3.8 25.6 - - + +
409X GLY* 3.5 27.4 - - - +
413X GLN* 3.9 11.7 + - - +
414X GLY* 3.9 18.2 - - - +
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Residues in contact with ALA 182 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177U ILE* 4.3 5.8 - - + +
178U LEU 3.0 11.5 + - - +
179U VAL* 3.2 11.3 + - - +
181U LEU* 1.3 76.4 - - - +
183U SER* 1.3 65.1 + - - +
184U GLU 3.3 2.5 - - - -
185U GLN* 2.9 33.1 + - + +
137X LYS* 3.2 38.4 - - + +
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Residues in contact with SER 183 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179U VAL 4.3 3.2 + - - -
180U HIS 5.3 2.9 - - - -
181U LEU* 3.1 5.7 - - - -
182U ALA* 1.3 78.1 - - - +
184U GLU* 1.3 62.5 + - - +
185U GLN 3.1 6.2 + - - -
186U LEU* 3.9 15.8 - - - +
413X GLN* 5.1 14.4 - - - -
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Residues in contact with GLU 184 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181U LEU 4.3 5.4 + - - +
182U ALA 3.3 0.6 - - - -
183U SER* 1.3 77.8 + - - +
185U GLN* 1.3 57.1 + - - +
186U LEU* 3.3 16.4 + - - +
187U GLU* 4.7 0.9 + - - +
192U LYS* 5.1 4.7 - - - +
353X ASN* 5.4 5.2 - - - +
354X VAL* 6.0 1.0 - - + +
413X GLN* 3.8 24.0 - - - +
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Residues in contact with GLN 185 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176U ASP* 3.7 7.4 + - - -
177U ILE* 3.2 26.2 - - + +
182U ALA* 2.9 18.3 + - - +
183U SER 4.3 0.2 - - - +
184U GLU* 1.3 75.4 - - - +
186U LEU* 1.3 60.0 + - - +
192U LYS* 2.9 50.3 + - + +
193U VAL* 3.4 18.2 - - - +
137X LYS* 2.7 34.6 + - - -
189X LYS* 4.1 14.1 - - + +
190X ALA* 4.9 3.1 + - - -
351X TYR* 4.2 5.1 + - - -
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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