Contacts of the helix formed by residues 141 - 153 (chain f) 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 ALA 141 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11f THR* 3.6 25.0 + - + +
139f GLY 3.4 0.2 - - - -
140f SER* 1.3 77.5 + - - +
142f SER* 1.3 64.6 + - - +
143f ALA 3.2 2.9 - - - -
144f MET* 2.9 22.2 + - - +
145f LEU* 3.0 12.9 + - + +
182f ALA* 3.9 16.4 - - + -
186f ASP* 3.3 26.9 + - + +
189f THR* 3.7 4.7 - - - +
144q GLU* 5.0 0.2 - - - -
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Residues in contact with SER 142 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25e TYR* 4.7 7.7 + - - -
11f THR* 4.5 1.0 - - - +
137f ALA* 2.7 38.0 + - - +
138f GLY* 3.7 10.6 - - - -
139f GLY 3.1 20.5 + - - -
140f SER 3.2 0.8 - - - -
141f ALA* 1.3 78.9 - - - +
143f ALA* 1.3 58.2 + - - +
145f LEU* 4.0 0.2 - - - +
146f GLN* 2.9 37.6 + - - +
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Residues in contact with ALA 143 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25e TYR* 4.0 34.5 - - + -
140f SER 4.6 0.4 + - - +
141f ALA 3.2 0.8 - - - -
142f SER* 1.3 79.4 - - - +
144f MET* 1.3 56.9 + - - +
147f PRO* 3.2 23.0 - - - +
144q GLU* 3.3 28.9 + - + +
145q GLN* 3.7 16.6 - - - +
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Residues in contact with MET 144 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141f ALA* 2.9 15.3 + - + +
143f ALA* 1.3 78.9 - - - +
145f LEU* 1.3 69.7 + - + +
147f PRO* 3.5 7.6 - - - +
148f LEU* 4.4 4.9 + - - +
181f SER 5.8 0.2 - - - -
182f ALA* 4.5 9.0 - - + -
185f ARG* 3.6 45.8 - - + +
186f ASP* 3.9 19.1 - - + +
25p VAL* 4.3 8.5 - - + -
144q GLU* 3.4 51.6 - - + +
147q TYR* 4.9 1.6 - - + -
148q GLY* 3.6 32.8 - - - +
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Residues in contact with LEU 145 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11f THR* 3.7 24.7 - - + -
12f ILE 4.6 0.2 - - - +
13f LEU* 4.1 21.5 - - + -
137f ALA* 3.7 23.8 - - + -
141f ALA 3.0 12.4 + - - +
144f MET* 1.3 81.0 - - + +
146f GLN* 1.3 65.3 + - - +
148f LEU* 3.2 15.6 + - - +
149f LEU* 3.2 23.1 + - + +
178f VAL* 3.4 39.0 - - + +
179f PHE* 4.4 9.2 - - + -
182f ALA* 3.7 16.8 - - + -
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Residues in contact with GLN 146 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25e TYR* 2.7 31.2 - - + +
27e ALA 4.7 0.7 - - - +
135f PHE* 3.7 11.4 + - - +
136f LYS* 3.3 26.4 - - - +
137f ALA* 3.1 29.4 - - + +
142f SER* 2.9 25.1 + - - +
145f LEU* 1.3 77.3 - - - +
147f PRO* 1.3 65.1 - - + +
149f LEU* 3.4 6.1 + - - +
150f ASP* 3.0 36.2 + - - +
177q ARG* 3.1 33.5 + - - -
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Residues in contact with PRO 147 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25e TYR* 5.2 0.2 - - - +
143f ALA 3.2 24.7 - - - +
144f MET 3.5 7.0 - - - +
145f LEU 3.4 4.3 - - - -
146f GLN* 1.3 93.9 - - + +
148f LEU* 1.3 61.6 + - - +
150f ASP* 3.3 11.9 + - + +
151f ASN* 3.1 20.6 + - - +
145q GLN* 4.1 22.4 - - + +
149q MET* 3.5 27.0 - - + +
173q ASN* 3.8 22.3 - - - +
177q ARG* 4.6 5.8 - - + -
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Residues in contact with LEU 148 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144f MET 4.4 5.1 + - - +
145f LEU 3.2 9.2 + - - +
147f PRO* 1.3 77.3 - - - +
149f LEU* 1.3 57.1 + - - +
151f ASN* 2.8 14.0 + - - +
152f GLN* 2.7 55.8 + - + +
174f LEU* 4.6 10.5 - - + -
177f ASP* 5.7 0.7 - - + -
178f VAL* 3.5 27.6 - - + +
202p TYR* 4.8 9.9 - - + +
148q GLY 5.2 1.6 - - - +
149q MET* 3.5 18.3 - - + -
152q SER* 3.4 37.9 - - - +
153q LEU* 4.7 8.7 - - + -
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Residues in contact with LEU 149 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13f LEU* 3.4 36.6 - - + -
15f ILE* 4.3 12.3 - - + -
135f PHE* 3.3 30.8 - - + -
137f ALA* 4.5 0.7 - - + +
145f LEU* 3.2 26.8 + - + +
146f GLN* 3.7 13.5 - - - +
148f LEU* 1.3 76.8 - - + +
150f ASP* 1.3 61.6 + - - +
152f GLN* 5.2 0.7 - - - -
153f VAL* 3.0 33.8 + - + +
154f GLY 3.2 2.3 + - - -
174f LEU* 4.1 23.3 - - + -
178f VAL* 4.4 16.4 - - + -
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Residues in contact with ASP 150 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135f PHE* 3.2 23.9 - - - -
146f GLN* 3.0 18.7 + - - +
147f PRO* 3.4 10.8 - - + +
149f LEU* 1.3 77.2 - - - +
151f ASN* 1.3 58.8 + - - +
154f GLY* 3.5 2.3 + - - -
155f PHE 3.5 5.2 + - - -
156f LYS* 3.2 43.5 + - + +
173q ASN* 4.4 7.4 - - + +
177q ARG* 2.5 56.3 + - - +
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Residues in contact with ASN 151 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147f PRO 3.1 11.1 + - - +
148f LEU* 2.8 11.7 + - + +
150f ASP* 1.3 78.5 - - - +
152f GLN* 1.3 82.7 + - - +
155f PHE* 3.2 24.9 + - - -
156f LYS 3.3 13.3 + - - -
158f MET* 3.4 21.8 - - - +
204p CYS* 6.0 1.0 - - - -
149q MET* 4.1 13.3 - - + +
153q LEU* 4.4 7.3 - - - +
169q GLN* 2.9 29.0 + - - +
173q ASN* 3.5 19.1 - - - +
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Residues in contact with GLN 152 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148f LEU* 2.7 36.8 + - + +
151f ASN* 1.3 98.8 + - - +
153f VAL* 1.3 59.8 + - + +
155f PHE* 3.8 9.4 - - - -
158f MET* 4.9 11.5 - - - +
170f ARG* 3.0 46.1 + - - +
174f LEU* 4.2 16.4 - - + -
202p TYR* 3.0 58.6 + - + +
204p CYS* 5.7 2.2 - - - -
153q LEU* 4.8 2.8 - - - +
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Residues in contact with VAL 153 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15f ILE* 4.4 19.3 - - + -
16f ALA 6.0 0.9 - - - +
134f SER* 5.7 2.0 - - - -
135f PHE* 3.8 22.2 - - + -
149f LEU* 3.0 24.0 + - + +
152f GLN* 1.3 80.9 - - - +
154f GLY* 1.3 58.9 + - - +
155f PHE* 3.4 19.7 - - - -
166f LEU* 5.4 11.0 - - + -
170f ARG* 4.9 4.9 - - - +
174f LEU* 3.4 32.8 - - + -
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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