Contacts of the helix formed by residues 177 - 188 (chain N) 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 LEU 177 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168N LEU* 4.7 13.7 - - + -
176N MET* 1.3 86.9 - - + +
178N ALA* 1.3 58.3 + - - +
179N TYR 3.1 1.7 - - - +
180N SER* 2.8 7.3 + - - -
181N LEU* 2.2 42.0 + - + +
201N LEU* 5.1 14.1 - - + +
204N ILE* 4.5 22.4 - - + -
205N TYR* 5.7 7.9 - - + -
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Residues in contact with ALA 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175N GLY* 5.9 4.9 - - - +
176N MET 4.8 0.4 - - - +
177N LEU* 1.3 76.1 - - - +
179N TYR* 1.3 60.4 + - + +
181N LEU* 3.6 13.8 - - + +
182N LYS* 2.4 42.0 + - + +
215N ASN* 5.5 11.6 - - - -
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Residues in contact with TYR 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148N LYS* 2.4 48.6 + - + -
175N GLY* 4.9 19.9 - - - -
176N MET* 5.0 7.5 - - - +
177N LEU 4.2 6.5 - - - +
178N ALA* 1.3 80.7 - - + +
180N SER* 1.3 59.2 + - - +
182N LYS* 4.4 2.4 - - - +
183N LEU* 3.1 22.3 + - - +
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Residues in contact with SER 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148N LYS* 4.8 6.5 - - - +
151N ILE* 4.5 23.1 - - - +
155N LEU* 5.1 10.0 - - - +
176N MET 4.7 8.3 - - - -
177N LEU* 2.8 11.6 + - - +
179N TYR* 1.3 75.3 - - - +
181N LEU* 1.3 54.6 + - - +
183N LEU* 3.0 9.0 + - - +
184N CYS* 2.3 43.3 + - - +
197N VAL* 6.1 1.0 - - - +
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Residues in contact with LEU 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177N LEU* 2.2 33.1 + - + +
178N ALA* 3.6 11.7 - - + +
180N SER* 1.3 64.1 - - - +
182N LYS* 1.3 71.9 + - + +
184N CYS* 2.9 18.0 + - - +
185N MET* 2.9 24.2 + - + +
197N VAL* 5.5 4.3 - - + -
198N LEU* 3.8 23.6 - - + +
201N LEU* 3.4 40.6 - - + -
215N ASN* 5.0 17.5 - - - +
218N GLN* 5.9 4.7 - - + -
219N CYS* 4.7 12.1 - - + +
222N PHE* 6.4 0.4 - - + -
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Residues in contact with LYS 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178N ALA* 2.4 33.8 + - + +
179N TYR* 4.4 2.9 - - - +
181N LEU* 1.3 78.1 - - + +
183N LEU* 1.3 62.9 + - - +
185N MET* 3.4 10.0 + - + +
186N SER* 3.2 22.4 + - - +
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Residues in contact with LEU 183 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K TYR* 4.4 24.9 - - + +
42K SER* 5.7 8.3 - - - -
46K LYS* 5.2 15.7 - - - +
148N LYS* 6.5 0.4 - - + -
155N LEU* 4.7 3.6 - - + -
179N TYR 3.1 17.6 + - - +
180N SER* 3.0 15.9 + - - +
181N LEU 3.0 0.2 - - - -
182N LYS* 1.3 79.8 - - - +
184N CYS* 1.3 53.1 + - - +
186N SER* 2.6 35.1 + - - +
187N LEU* 2.9 35.8 + - + +
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Residues in contact with CYS 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155N LEU* 5.0 14.8 - - + +
180N SER* 2.3 32.6 + - - +
181N LEU* 2.9 11.4 + - + +
183N LEU* 1.3 66.6 - - - +
185N MET* 1.3 63.7 + - - +
187N LEU* 2.9 16.1 + - - +
188N MET* 3.0 14.3 + - + +
193N PHE* 6.4 0.2 - - + -
194N ARG* 3.2 30.7 + - + +
197N VAL* 5.0 11.7 - - + -
198N LEU* 6.0 0.4 - - + -
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Residues in contact with MET 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181N LEU* 2.9 29.5 + - + +
182N LYS* 3.4 11.9 - - + +
183N LEU 3.0 0.2 + - - -
184N CYS* 1.3 74.9 - - - +
186N SER* 1.3 62.9 + - - +
194N ARG* 2.7 35.1 + - - +
198N LEU* 5.1 5.4 - - + -
218N GLN* 5.8 3.4 - - + -
222N PHE* 4.6 20.2 - - + -
593N SER* 6.1 0.5 - - - -
628N ARG* 4.8 12.0 + - - +
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Residues in contact with SER 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49K GLN* 5.8 1.6 + - - -
182N LYS* 3.2 14.1 + - - +
183N LEU* 2.6 25.3 + - - +
185N MET* 1.3 74.9 - - - +
187N LEU* 1.3 63.2 + - - +
593N SER* 5.6 1.7 + - - -
628N ARG* 6.2 0.4 - - - +
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Residues in contact with LEU 187 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K TYR* 4.9 6.3 - - + +
45K LYS* 6.5 0.9 - - + -
46K LYS* 6.5 0.4 - - - -
155N LEU* 4.8 14.4 - - + -
183N LEU* 2.9 47.5 + - + +
184N CYS* 2.9 6.8 + - - +
185N MET 4.7 0.7 - - - -
186N SER* 1.3 85.2 - - - +
188N MET* 1.3 70.5 + - - +
189N GLN* 3.2 6.1 + - - +
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Residues in contact with MET 188 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41K TYR* 5.9 1.1 - - - -
155N LEU* 4.9 8.5 - - + -
184N CYS* 3.0 10.2 + - + +
187N LEU* 1.3 76.8 - - - +
189N GLN* 1.3 70.9 + - - +
190N ASN* 3.0 29.8 - - + +
193N PHE* 3.4 33.4 - - + -
194N ARG* 3.9 32.6 + - + +
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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