Contacts of the helix formed by residues 178 - 185 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176I ASP 3.4 2.5 + - - -
177I ILE* 1.3 88.0 - - + +
179I VAL* 1.3 66.5 + - - +
180I HIS* 3.5 35.7 - - + +
181I LEU* 3.0 20.9 + - + +
182I ALA* 3.0 17.0 + - - +
137L LYS* 5.4 0.2 - - - -
345L ALA* 3.4 34.3 - - + -
346L ALA 6.1 0.2 - - - +
355L MET* 5.6 5.6 - - + -
408L LEU* 4.4 5.8 - - + -
439L ASN* 4.7 3.6 - - - +
440L MSE 3.8 43.1 - - + +
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Residues in contact with VAL 179 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177I ILE 3.7 0.6 + - - -
178I LEU* 1.3 72.6 - - - +
180I HIS* 1.3 81.5 + - + +
181I LEU 3.1 1.0 + - - -
182I ALA* 3.2 19.7 + - - +
183I SER* 4.2 3.6 + - - -
134L GLY 4.0 16.4 - - - +
135L ILE* 3.3 27.1 - - - +
136L LYS* 3.6 17.1 - - + +
137L LYS* 3.4 25.4 - - + +
440L MSE 4.7 3.4 + - - +
441L HIS* 4.3 18.6 - - + +
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Residues in contact with HIS 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178I LEU* 3.0 27.8 + - + -
179I VAL* 1.3 87.2 - - + +
181I LEU* 1.3 71.4 + - + +
183I SER* 5.1 4.0 + - - -
296L GLU* 5.2 0.2 - - - -
408L LEU* 4.4 12.8 - - + -
414L GLY* 3.1 23.0 - - - -
415L GLY 3.9 11.7 + - - +
440L MSE 3.0 32.0 - - + +
441L HIS* 3.4 26.3 + + - -
6023L MN 4.5 2.0 - - - -
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Residues in contact with LEU 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I ILE* 4.3 6.8 - - + +
178I LEU* 3.0 23.6 + - + -
180I HIS* 1.3 95.7 - - + +
182I ALA* 1.3 56.4 + - - +
183I SER* 3.1 9.7 + - - +
184I GLU* 4.4 4.3 + - - +
345L ALA* 5.6 0.2 - - + -
354L VAL* 3.5 47.2 - - + +
355L MET* 4.1 7.4 - - + -
408L LEU* 3.7 26.9 - - + +
409L GLY* 3.6 27.1 - - - +
413L GLN* 3.9 11.7 + - + +
414L GLY* 3.9 17.7 - - - +
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Residues in contact with ALA 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177I ILE* 4.4 5.4 - - + +
178I LEU 3.0 10.6 + - - +
179I VAL* 3.2 11.8 + - - +
181I LEU* 1.3 76.4 - - - +
183I SER* 1.3 63.1 + - - +
184I GLU 3.3 2.5 - - - -
185I GLN* 2.9 32.3 + - - +
137L LYS* 3.2 39.0 - - + +
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Residues in contact with SER 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179I VAL 4.2 3.4 + - - -
180I HIS 5.3 2.9 - - - -
181I LEU* 3.1 6.3 - - - +
182I ALA* 1.3 77.9 - - - +
184I GLU* 1.3 63.5 + - - +
185I GLN 3.1 1.2 + - - -
186I LEU* 3.9 21.0 - - - +
413L GLN* 5.1 14.6 - - - -
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Residues in contact with GLU 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181I LEU 4.4 5.4 + - - +
182I ALA 3.3 0.8 - - - -
183I SER* 1.3 78.8 + - - +
185I GLN* 1.3 55.7 + - - +
186I LEU* 3.3 15.5 + - - +
187I GLU* 4.7 1.0 + - - +
192I LYS* 5.1 4.5 - - - +
353L ASN* 5.5 3.1 - - - +
354L VAL* 6.1 1.0 - - + -
413L GLN* 3.8 25.3 - - - +
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Residues in contact with GLN 185 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176I ASP* 3.7 7.7 + - - -
177I ILE* 3.3 25.3 - - + +
182I ALA* 2.9 17.6 + - - +
184I GLU* 1.3 75.5 - - - +
186I LEU* 1.3 58.0 + - - +
192I LYS* 2.9 49.8 + - + +
193I VAL* 3.4 18.8 - - - +
137L LYS* 2.6 35.7 + - - -
189L LYS* 4.1 14.2 - - + +
190L ALA* 4.8 3.8 + - - -
351L TYR* 4.4 4.2 + - - -
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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