Contacts of the helix formed by residues 121 - 138 (chain G) in PDB entry 5JGH
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 GLY 121 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G ALA* 1.3 77.5 - - - +
122G PRO* 1.3 76.3 - - - +
123G PHE 3.4 2.5 - - - -
124G ILE* 3.1 19.7 + - - +
125G LYS* 3.1 13.1 + - - +
169G TYR* 3.8 7.2 - - - -
201G ACT 3.2 21.2 + - - -
4H A 6.2 0.7 - - - -
5H T 4.9 5.4 - - - -
19I T 4.9 1.0 + - - -
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Residues in contact with PRO 122 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G GLY* 1.3 83.6 - - - +
123G PHE* 1.3 63.3 + - - +
125G LYS* 3.5 4.3 + - - +
126G TYR* 2.9 23.7 + - - +
154G TRP* 3.8 18.4 - - + -
165G TYR* 3.7 39.0 - - + +
166G ILE* 3.8 16.6 - - + +
169G TYR* 3.8 10.3 - - + -
5H T 3.6 29.4 - - - +
6H T 4.0 12.1 - - - +
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Residues in contact with PHE 123 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G GLY 3.4 0.8 - - - -
122G PRO* 1.3 79.3 - - - +
124G ILE* 1.3 67.8 + - + +
126G TYR* 3.2 1.4 + + - +
127G ALA* 2.7 40.9 + - + +
147G MET* 4.1 5.2 - - - -
150G ILE* 3.5 42.6 - - + -
151G GLY* 3.5 19.7 - - - -
154G TRP* 3.5 28.1 - + + -
3H T 3.7 34.3 - - + -
4H A 3.1 48.2 + - - +
5H T 4.5 5.5 + - - -
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Residues in contact with ILE 124 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ALA* 4.0 15.0 - - + -
121G GLY 3.1 15.3 + - - +
123G PHE* 1.3 93.0 - - + +
125G LYS* 1.3 64.2 + - - +
127G ALA* 3.2 4.8 + - + +
128G ASN* 2.9 25.3 + - + +
147G MET* 5.9 0.4 - - + -
3H T 4.1 3.8 - - - +
4H A 4.2 12.1 - - + -
19I T 3.6 26.2 - - + +
20I A 3.5 61.2 - - + +
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Residues in contact with LYS 125 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ALA* 3.5 25.2 + - + +
121G GLY 3.1 11.5 + - - +
122G PRO* 3.8 5.2 - - - +
124G ILE* 1.3 75.7 - - - +
126G TYR* 1.3 63.8 + - - +
128G ASN* 3.2 13.7 + - - +
129G GLU* 3.2 19.5 + - - +
165G TYR* 4.1 17.5 - - + -
168G GLU* 3.1 29.8 + - - +
169G TYR* 3.0 40.9 - - - +
172G ALA* 3.9 11.7 - - - +
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Residues in contact with TYR 126 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G PRO 2.9 17.8 + - - +
123G PHE* 3.6 4.3 - + - +
125G LYS* 1.3 76.1 - - - +
127G ALA* 1.3 67.4 + - - +
129G GLU* 3.0 12.3 + - - -
130G VAL* 3.1 34.1 + - + +
150G ILE* 4.0 19.3 - - + -
153G LYS* 3.3 33.1 + - - +
154G TRP* 3.5 46.2 - + + -
157G LEU* 3.4 24.2 - - + +
161G ILE* 6.0 0.4 - - + -
165G TYR* 3.4 39.6 - + + -
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Residues in contact with ALA 127 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G PHE* 2.7 33.9 + - + +
124G ILE* 3.7 5.4 - - + +
126G TYR* 1.3 73.7 - - - +
128G ASN* 1.3 62.3 + - - +
130G VAL* 3.7 1.2 - - - +
131G ARG* 2.9 26.9 + - - +
147G MET* 4.2 20.5 - - + +
150G ILE* 3.5 33.8 - - + +
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Residues in contact with ASN 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ILE* 2.9 18.9 + - + +
125G LYS* 3.6 7.9 - - - +
126G TYR 3.1 0.4 - - - -
127G ALA* 1.3 78.6 - - - +
129G GLU* 1.3 63.5 + - + +
130G VAL 3.3 0.7 + - - -
131G ARG* 3.5 15.4 + - - +
132G SER* 4.9 1.6 + - - -
20I A 4.5 2.6 + - - -
21I A 3.6 36.2 + - - +
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Residues in contact with GLU 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125G LYS* 3.4 10.9 - - + +
126G TYR 3.0 7.2 + - - +
128G ASN* 1.3 78.8 - - + +
130G VAL* 1.3 64.7 + - + +
132G SER* 4.7 6.9 + - - -
133G GLN* 5.6 0.9 + - - +
165G TYR* 2.9 38.4 + - - -
168G GLU* 4.7 10.6 - - - +
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Residues in contact with VAL 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G TYR* 3.1 47.7 + - + +
127G ALA* 3.7 3.6 - - - +
129G GLU* 1.3 84.2 - - + +
131G ARG* 1.3 66.8 + - - +
132G SER 3.3 2.8 + - - -
133G GLN* 3.4 13.5 + - + +
134G VAL* 3.0 38.8 + - + +
150G ILE* 4.7 3.4 - - + -
153G LYS* 3.7 18.6 - - + +
165G TYR* 5.0 2.0 - - - +
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Residues in contact with ARG 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G ALA 2.9 17.0 + - - +
128G ASN* 3.5 13.8 + - - +
130G VAL* 1.3 77.7 - - - +
132G SER* 1.3 66.7 + - - +
134G VAL* 3.2 1.6 + - - +
135G PHE* 2.8 62.4 + - - +
143G GLN* 3.4 34.0 + - - +
146G LEU* 3.7 19.3 - - + +
147G MET* 5.8 1.8 - - + -
150G ILE* 4.1 13.2 - - + -
21I A 4.6 6.3 - - - -
22I A 3.7 36.5 + - - -
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Residues in contact with SER 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G ASN 4.9 1.3 + - - -
129G GLU 4.7 8.1 + - - -
131G ARG* 1.3 89.8 - - - +
133G GLN* 1.3 59.2 + - - +
135G PHE* 3.3 6.6 + - - +
136G ALA* 2.9 28.5 + - - +
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Residues in contact with GLN 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129G GLU 6.0 0.4 - - - +
130G VAL* 3.4 14.9 + - + +
131G ARG 3.3 0.6 - - - -
132G SER* 1.3 77.9 + - - +
134G VAL* 1.3 67.4 + - - +
136G ALA* 3.3 8.6 + - + +
137G GLN* 3.1 39.1 + - - +
153G LYS* 6.2 1.6 - - - -
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Residues in contact with VAL 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G VAL* 3.0 39.4 + - + +
131G ARG 3.7 2.7 - - - +
133G GLN* 1.3 76.3 - - - +
135G PHE* 1.3 58.8 + - - +
137G GLN* 3.1 14.0 - - - +
138G HIS* 3.0 36.7 + - + +
146G LEU* 3.5 23.3 - - + -
149G ILE* 4.1 10.1 - - + -
150G ILE* 4.0 21.5 - - + -
153G LYS* 3.5 25.8 - - + +
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Residues in contact with PHE 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131G ARG* 2.8 43.1 + - - +
132G SER* 3.8 4.5 - - - +
134G VAL* 1.3 77.1 - - - +
136G ALA* 1.3 65.9 + - - +
138G HIS 3.0 29.5 + - - -
139G PRO* 3.1 42.0 - - + +
141G LYS 3.8 16.6 - - - -
146G LEU* 3.6 20.2 - - + +
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Residues in contact with ALA 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G SER 2.9 17.3 + - - +
133G GLN* 3.6 10.8 - - + +
134G VAL 3.2 0.4 - - - -
135G PHE* 1.3 81.2 - - - +
137G GLN* 1.3 60.7 + - - +
139G PRO* 4.1 12.0 - - - +
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Residues in contact with GLN 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G GLN* 3.1 32.3 + - - +
134G VAL* 3.1 26.3 - - - +
136G ALA* 1.3 76.2 - - - +
138G HIS* 1.3 83.7 + - + +
139G PRO* 3.7 6.5 - - - +
149G ILE* 5.7 0.3 - - - +
153G LYS* 4.0 20.2 + - - +
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Residues in contact with HIS 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D GLN* 3.2 32.4 + - + +
134G VAL* 3.0 33.5 + - + +
135G PHE* 3.0 15.8 + - - +
137G GLN* 1.3 108.2 + - + +
139G PRO* 1.3 65.3 - - - +
140G ASP* 3.2 7.5 + - - -
141G LYS* 3.3 26.8 + - + +
146G LEU* 4.2 10.9 - - + +
149G ILE* 3.8 30.1 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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