Contacts of the helix formed by residues 178 - 185 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176S ASP 3.4 3.6 + - - -
177S ILE* 1.3 88.0 - - + +
179S VAL* 1.3 67.0 + - - +
180S HIS* 3.0 36.3 - - + +
181S LEU* 3.0 21.1 + - + +
182S ALA* 3.0 17.3 + - - +
137V LYS* 5.3 0.4 - - - -
345V ALA* 3.5 31.0 - - + -
355V MET* 5.5 6.5 - - + -
408V LEU* 4.3 7.2 - - + -
439V ASN* 4.9 2.5 - - - +
440V MSE 4.1 40.6 - - + +
441V HIS* 6.4 0.2 - - + -
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Residues in contact with VAL 179 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177S ILE 3.7 1.0 + - - -
178S LEU* 1.3 73.5 - - - +
180S HIS* 1.3 86.0 + - + +
181S LEU 3.1 1.0 + - - -
182S ALA* 3.2 19.5 + - - +
183S SER* 4.3 3.5 + - - -
134V GLY 4.2 11.7 - - - +
135V ILE* 3.4 19.7 - - - +
136V LYS* 3.5 21.8 - - + +
137V LYS* 3.2 33.8 - - + +
440V MSE 5.0 2.8 + - - +
441V HIS* 4.6 11.9 - - + +
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Residues in contact with HIS 180 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178S LEU* 3.0 28.6 - - + -
179S VAL* 1.3 88.1 - - + +
181S LEU* 1.3 72.2 + - + +
183S SER* 5.1 4.5 + - - -
134V GLY 5.9 0.2 - - - -
408V LEU* 4.5 11.2 - - + -
413V GLN 4.6 0.3 - - - +
414V GLY* 3.0 22.3 - - - -
415V GLY 4.0 15.4 + - - +
440V MSE 3.3 30.7 - - + +
441V HIS* 3.6 25.1 + + - -
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Residues in contact with LEU 181 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177S ILE* 4.3 6.9 - - + +
178S LEU* 3.0 22.7 + - + -
180S HIS* 1.3 95.0 - - + +
182S ALA* 1.3 57.0 + - - +
183S SER* 3.1 10.0 + - - +
184S GLU* 4.3 5.2 + - - +
185S GLN 5.4 0.2 + - - -
345V ALA* 5.9 0.2 - - + -
354V VAL* 3.2 58.1 - - + +
355V MET* 4.2 6.3 - - + -
408V LEU* 4.0 21.8 - - + +
409V GLY* 3.6 17.0 - - - +
413V GLN* 3.9 12.5 + - - +
414V GLY* 3.7 21.5 - - - +
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Residues in contact with ALA 182 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177S ILE* 4.4 5.6 - - + +
178S LEU 3.0 9.7 + - - +
179S VAL* 3.2 11.2 + - - +
181S LEU* 1.3 76.8 - - - +
183S SER* 1.3 58.6 + - - +
184S GLU 3.3 2.0 - - - -
185S GLN* 2.8 40.3 + - - +
137V LYS* 3.3 37.9 - - + +
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Residues in contact with SER 183 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179S VAL 4.3 3.9 + - - -
180S HIS 5.3 3.6 - - - -
181S LEU* 3.1 5.6 - - - -
182S ALA* 1.3 78.7 - - - +
184S GLU* 1.3 62.1 + - - +
185S GLN 3.1 1.0 + - - -
186S LEU* 3.9 20.6 - - - +
413V GLN* 5.2 12.8 - - - -
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Residues in contact with GLU 184 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181S LEU 4.3 5.4 + - - +
182S ALA 3.3 0.6 - - - -
183S SER* 1.3 79.2 - - - +
185S GLN* 1.3 56.9 + - - +
186S LEU* 3.3 16.1 + - - +
187S GLU* 4.7 1.0 + - - +
192S LYS* 5.1 4.9 - - - +
353V ASN* 5.6 2.8 - - - +
413V GLN* 4.1 21.8 - - - +
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Residues in contact with GLN 185 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176S ASP* 3.6 8.1 + - - -
177S ILE* 3.2 24.4 - - + +
181S LEU 5.4 0.2 + - - -
182S ALA* 2.8 20.7 + - - +
184S GLU* 1.3 77.4 - - - +
186S LEU* 1.3 57.4 + - - +
192S LYS* 2.9 49.7 + - + +
193S VAL* 3.4 19.0 - - - +
137V LYS* 2.9 33.3 + - - -
189V LYS* 4.0 13.9 - - + +
190V ALA* 4.7 3.8 + - - -
351V TYR* 4.4 4.8 + - - -
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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