Contacts of the helix formed by residues 178 - 185 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345I ALA* 3.5 33.9 - - + -
355I MET* 5.6 5.2 - - + -
408I LEU* 4.3 6.3 - - + -
439I ASN* 4.8 2.7 - - - +
440I MSE 3.9 42.6 - - + +
176L ASP 3.5 2.3 + - - -
177L ILE* 1.3 86.9 - - + +
179L VAL* 1.3 67.7 + - - +
180L HIS* 3.0 36.1 - - + +
181L LEU* 3.0 27.4 + - + +
182L ALA* 3.0 9.4 + - - +
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Residues in contact with VAL 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I GLY 4.0 16.2 - - - +
135I ILE* 3.3 27.4 - - - +
136I LYS* 3.6 18.5 - - + +
137I LYS* 3.4 24.7 - - + +
440I MSE 4.8 3.4 + - - +
441I HIS* 4.4 12.8 - - + +
177L ILE 3.7 0.8 + - - -
178L LEU* 1.3 71.8 - - - +
180L HIS* 1.3 85.5 + - + +
181L LEU 3.1 0.7 + - - -
182L ALA* 3.2 20.6 + - - +
183L SER* 4.2 3.3 + - - -
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Residues in contact with HIS 180 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296I GLU* 5.3 0.7 - - - -
408I LEU* 4.4 12.1 - - + -
414I GLY* 3.0 22.5 - - - -
415I GLY 3.9 13.7 + - - +
440I MSE 3.1 31.1 - - + +
441I HIS* 3.4 26.0 + + - -
178L LEU* 3.0 28.0 + - + -
179L VAL* 1.3 86.8 - - + +
181L LEU* 1.3 70.3 + - + +
183L SER* 5.0 3.6 + - - -
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Residues in contact with LEU 181 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345I ALA* 5.7 0.2 - - + -
354I VAL* 3.5 46.6 - - + +
355I MET* 4.2 7.0 - - + -
408I LEU* 3.8 25.8 - - + -
409I GLY* 3.6 27.8 - - - +
413I GLN* 3.8 11.8 + - + +
414I GLY* 3.8 20.0 - - - +
177L ILE* 4.3 7.2 - - + +
178L LEU* 3.0 23.8 + - + -
180L HIS* 1.3 93.9 - - + +
182L ALA* 1.3 57.5 + - - +
183L SER* 3.1 9.7 + - - +
184L GLU* 4.4 4.2 + - - +
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Residues in contact with ALA 182 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I LYS* 3.3 35.7 - - + +
177L ILE* 4.5 5.8 - - + -
178L LEU 3.0 11.1 + - - +
179L VAL* 3.2 11.1 + - - +
181L LEU* 1.3 74.9 - - - +
183L SER* 1.3 64.6 + - - +
184L GLU 3.3 2.2 - - - -
185L GLN* 2.8 35.8 + - - +
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Residues in contact with SER 183 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413I GLN* 5.1 13.9 - - - -
179L VAL 4.2 3.2 + - - -
180L HIS 5.3 3.6 - - - -
181L LEU* 3.1 6.1 - - - -
182L ALA* 1.3 78.4 - - - +
184L GLU* 1.3 63.2 + - - +
185L GLN 3.1 1.0 + - - -
186L LEU* 3.9 20.8 - - - +
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Residues in contact with GLU 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353I ASN 5.5 2.1 - - - +
354I VAL* 6.1 0.8 - - + +
413I GLN* 3.8 24.5 - - - +
181L LEU 4.4 5.6 + - - +
182L ALA 3.3 0.8 - - - -
183L SER* 1.3 78.7 + - - +
185L GLN* 1.3 56.5 + - - +
186L LEU* 3.3 17.2 + - - +
187L GLU* 4.7 0.9 + - - +
192L LYS* 5.0 4.3 - - - +
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Residues in contact with GLN 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137I LYS* 2.7 34.7 + - - -
189I LYS* 4.1 13.4 - - + +
190I ALA* 4.8 3.6 + - - -
351I TYR* 4.5 4.6 + - - -
176L ASP* 3.7 7.1 + - - -
177L ILE* 3.2 23.5 - - + +
182L ALA* 2.8 19.4 + - - +
184L GLU* 1.3 75.2 - - - +
186L LEU* 1.3 58.9 + - - +
192L LYS* 2.9 49.4 + - + +
193L VAL* 3.4 19.4 - - - +
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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