Contacts of the helix formed by residues 164 - 175 (chain m) 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 ARG 164 (chain m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421M MET* 6.1 6.3 - - + -
49m LEU* 5.2 4.0 - - - +
51m ARG* 6.2 0.4 - - - +
162m GLY 3.4 1.4 + - - -
163m ALA* 1.3 87.8 + - + +
165m SER* 1.3 61.1 + - - +
166m GLN* 3.3 5.1 + - - +
167m SER* 3.8 13.3 + - - +
198m THR* 3.2 50.0 + - - +
199m LEU* 3.8 15.9 - - - +
200m PRO* 4.2 16.5 - - - +
203m GLN* 4.3 4.4 + - - -
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Residues in contact with SER 165 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34m ALA* 4.8 1.3 - - - -
160m SER* 3.4 24.8 + - - -
161m ILE* 3.5 19.4 - - - -
162m GLY 2.6 28.0 + - - -
163m ALA 3.1 2.2 - - - -
164m ARG* 1.3 75.6 - - - +
166m GLN* 1.3 69.5 + - - +
167m SER 3.1 2.5 - - - -
168m ALA* 3.2 4.0 + - - +
169m ARG* 2.9 28.7 + - - +
198m THR* 4.5 5.6 - - - -
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Residues in contact with GLN 166 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383M GLU* 5.4 5.2 - - + +
386M ARG* 3.4 24.7 + - - +
387M CYS* 4.4 31.0 - - + +
421M MET* 5.6 7.0 - - + -
30m LYS* 5.5 8.1 - - - +
164m ARG* 3.3 2.8 - - - -
165m SER* 1.3 85.5 + - - +
167m SER* 1.3 56.8 + - - +
169m ARG* 3.2 44.7 + - - +
170m THR* 2.6 33.6 + - - -
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Residues in contact with SER 167 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383M GLU* 5.7 4.3 - - - -
417M HIS* 5.7 3.5 + - - -
421M MET* 6.1 1.2 - - - +
164m ARG* 3.8 13.8 + - - +
166m GLN* 1.3 77.8 - - - +
168m ALA* 1.3 62.6 + - - +
170m THR* 3.0 9.6 + - - -
171m TYR* 2.9 19.6 + - - +
197m GLU* 2.9 47.8 + - - +
198m THR* 4.8 0.3 - - - -
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Residues in contact with ALA 168 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36m VAL* 3.8 8.7 - - + -
160m SER* 3.4 25.6 - - - +
165m SER 3.2 4.3 + - - +
167m SER* 1.3 78.9 - - - +
169m ARG* 1.3 64.1 + - - +
171m TYR* 3.3 2.4 + - - +
172m LEU* 2.9 31.8 + - - +
194m ALA* 3.3 30.7 - - + +
197m GLU* 4.8 0.2 - - - -
198m THR* 3.7 11.8 - - + +
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Residues in contact with ARG 169 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386M ARG* 4.8 11.5 - - - +
146m GLN* 4.2 9.9 - - - +
159m MET* 2.9 32.8 - - + +
160m SER* 3.8 20.2 + - - +
161m ILE* 5.2 2.2 - - - +
165m SER* 2.9 15.7 + - - +
166m GLN* 3.3 42.1 + - - +
167m SER 3.2 0.2 - - - -
168m ALA* 1.3 77.3 - - - +
170m THR* 1.3 56.4 + - - +
172m LEU* 3.6 4.3 + - - +
173m GLU* 3.0 30.8 + - - +
54n LEU 5.9 0.2 + - - -
55n SER* 4.9 10.6 - - - -
57n LEU* 3.1 33.0 - - + +
58n TYR* 4.4 9.7 + - - -
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Residues in contact with THR 170 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380M ASN* 4.0 13.9 - - - +
383M GLU* 3.6 24.8 + - - +
386M ARG* 2.7 23.4 + - - +
166m GLN 2.6 23.0 + - - -
167m SER* 3.0 8.7 + - - -
169m ARG* 1.3 74.1 - - - +
171m TYR* 1.3 67.2 + - - +
173m GLU* 3.0 23.8 + - + +
174m ARG* 3.0 17.0 + - + +
197m GLU* 4.9 2.7 - - - -
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Residues in contact with TYR 171 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167m SER 2.9 8.4 + - - +
168m ALA* 3.8 7.6 - - - +
170m THR* 1.3 74.9 - - - +
172m LEU* 1.3 71.9 + - + +
174m ARG* 2.9 20.3 + - + +
175m HIS* 3.2 49.8 + + + -
179m PHE* 5.1 0.4 - + - -
190m HIS* 3.1 50.4 - + + -
193m ARG* 3.4 30.2 + - + +
194m ALA* 3.7 24.5 - - + -
197m GLU* 3.7 28.2 + - - +
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Residues in contact with LEU 172 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36m VAL* 3.6 23.3 - - + -
38m LEU* 3.8 28.7 - - + -
158m ALA* 4.2 6.3 - - + -
159m MET* 3.6 31.4 - - - +
160m SER* 4.3 1.6 - - - -
168m ALA 2.9 28.5 + - - +
169m ARG* 3.8 6.5 - - - +
171m TYR* 1.3 81.6 - - + +
173m GLU* 1.3 63.1 + - - +
174m ARG 3.1 1.0 + - - -
175m HIS 3.2 9.4 + - - -
176m MET* 3.2 20.2 + - - +
179m PHE* 3.7 13.5 - - + -
194m ALA* 3.7 21.5 - - + -
57n LEU* 3.8 9.9 - - + -
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Residues in contact with GLU 173 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386M ARG* 4.5 15.4 + - - -
169m ARG* 3.0 20.5 + - - +
170m THR* 3.0 16.9 + - - +
172m LEU* 1.3 76.6 - - - +
174m ARG* 1.3 58.0 + - - +
176m MET* 3.9 19.9 + - + +
55n SER* 4.3 7.4 + - - -
56n LYS* 3.3 46.8 + - + +
57n LEU* 3.9 7.4 - - + +
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Residues in contact with ARG 174 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170m THR* 3.0 12.8 + - + +
171m TYR* 2.9 18.2 + - - +
173m GLU* 1.3 81.1 - - - +
175m HIS* 1.3 82.5 + - + +
176m MET 3.5 1.2 + - - -
177m SER* 4.5 6.9 + - - -
178m GLU* 5.4 0.2 - - - +
197m GLU* 5.8 2.0 + - - -
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Residues in contact with HIS 175 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171m TYR* 3.2 48.9 + + + +
172m LEU 3.2 6.1 + - - -
174m ARG* 1.3 107.7 - - + +
176m MET* 1.3 62.5 - - - +
177m SER* 3.3 4.5 - - - +
178m GLU* 3.0 41.0 + - - +
179m PHE* 3.2 32.9 - - + -
190m HIS* 4.1 10.1 - - + -
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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