Contacts of the helix formed by residues 137 - 152 (chain G) in PDB entry 5GAD
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 ASP 137 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33G LEU* 3.9 24.9 - - + +
35G ARG* 4.9 11.2 + - - -
120G GLY 5.3 1.2 + - - -
121G ILE* 4.9 2.2 - - + +
135G GLY* 3.4 1.2 - - - -
136G ALA* 1.3 77.1 - - + +
138G LYS* 1.3 65.7 + - - +
139G GLN* 3.3 20.8 + - - +
140G VAL* 3.2 31.5 + - + +
141G ILE* 3.0 26.2 + - - +
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Residues in contact with LYS 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2746A U 3.8 32.4 - - - +
2747A G 3.1 27.9 + - - +
74G SER* 4.5 17.7 - - - +
83G PHE* 3.5 39.3 - - + -
136G ALA 3.5 5.5 + - - -
137G ASP* 1.3 71.7 + - - +
139G GLN* 1.3 65.7 + - - +
141G ILE* 3.1 10.5 - - + +
142G GLY* 2.9 22.3 + - - -
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Residues in contact with GLN 139 (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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2745A C 2.7 40.7 + - - +
2746A U 3.4 28.6 + - - +
2759A G 3.8 17.5 - - - +
2760A C 3.3 29.3 + - - +
35G ARG* 4.6 13.1 + - - +
137G ASP* 3.3 11.8 + - - +
138G LYS* 1.3 78.9 - - - +
140G VAL* 1.3 68.0 + - - +
143G GLN* 2.9 20.8 + - - +
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Residues in contact with VAL 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G PRO* 4.2 25.1 - - + -
119G ALA 5.1 4.9 - - - +
121G ILE* 4.2 12.6 - - + -
137G ASP* 3.2 35.4 + - + +
138G LYS 3.2 0.8 - - - -
139G GLN* 1.3 88.9 - - - +
141G ILE* 1.3 67.8 - - - +
143G GLN* 3.1 8.0 + - + +
144G VAL* 2.9 23.8 + - + +
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Residues in contact with ILE 141 (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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83G PHE* 3.8 22.7 - - + +
84G THR* 3.8 5.6 - - - -
85G LYS* 3.5 28.7 - - + +
121G ILE* 3.7 19.4 - - + +
133G LEU* 3.4 40.5 - - + +
135G GLY* 4.6 3.4 - - - +
137G ASP 3.0 20.3 + - - +
138G LYS* 3.1 19.7 - - + +
140G VAL* 1.3 74.8 - - - +
142G GLY* 1.3 63.5 + - - +
144G VAL* 3.4 4.6 + - - +
145G ALA* 2.9 23.2 + - - +
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Residues in contact with GLY 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2745A C 3.4 25.9 - - - +
2746A U 4.7 2.5 - - - -
85G LYS* 4.0 18.9 + - - -
138G LYS 2.9 14.1 + - - -
141G ILE* 1.3 79.2 - - - +
143G GLN* 1.3 60.5 + - - +
145G ALA* 3.4 2.9 - - - +
146G ALA* 3.0 22.7 + - - +
164G TYR* 5.1 0.3 + - - -
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Residues in contact with GLN 143 (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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2744A G 2.8 32.3 + - - +
2745A C 3.1 16.6 + - - +
2760A C 4.2 2.4 + - - +
2761A A 3.5 37.1 + - - +
139G GLN* 2.9 22.1 + - - +
140G VAL* 3.4 11.9 - - + +
142G GLY* 1.3 74.6 - - - +
144G VAL* 1.3 61.5 + - + +
146G ALA* 2.8 23.3 + - - +
147G ASP* 2.9 42.6 + - - +
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Residues in contact with VAL 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G HIS* 4.4 7.4 + - + +
117G LEU* 3.8 24.2 - - + -
118G PRO* 3.6 34.3 - - + -
121G ILE* 4.7 7.6 - - + -
133G LEU* 3.6 21.1 - - + -
140G VAL* 2.9 22.9 + - + +
141G ILE* 3.7 4.9 - - - +
143G GLN* 1.3 76.0 - - + +
145G ALA* 1.3 64.2 + - - +
147G ASP* 3.1 14.6 + - - +
148G LEU* 3.0 25.0 + - + +
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Residues in contact with ALA 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G LYS* 3.6 31.0 - - + +
87G LEU* 3.7 15.0 - - + +
133G LEU* 4.1 10.3 - - + +
141G ILE 2.9 17.8 + - - +
142G GLY 3.4 6.1 - - - +
144G VAL* 1.3 77.4 - - - +
146G ALA* 1.3 63.2 + - - +
148G LEU* 3.1 10.0 + - - +
149G ARG* 3.0 17.5 + - - +
164G TYR* 4.0 12.1 - - + -
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Residues in contact with ALA 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2744A G 3.8 22.7 - - - +
2745A C 3.9 11.7 - - - +
142G GLY 3.0 12.0 + - - +
143G GLN* 2.8 17.9 + - - +
145G ALA* 1.3 73.7 - - - +
147G ASP* 1.3 57.9 + - - +
149G ARG* 3.0 5.0 + - - +
150G ALA* 2.9 25.8 + - - +
164G TYR* 3.4 20.6 + - - +
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Residues in contact with ASP 147 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2761A A 4.7 4.1 + - - -
115G HIS* 3.5 27.3 + - + -
143G GLN* 2.9 52.9 + - - +
144G VAL* 3.1 10.2 + - - +
146G ALA* 1.3 73.8 - - - +
148G LEU* 1.3 65.3 + - - +
150G ALA* 3.1 23.0 + - - +
151G TYR* 3.7 13.9 + - - -
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Residues in contact with LEU 148 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87G LEU* 3.8 28.3 - - + -
103G ILE* 3.8 24.7 - - + -
105G LEU* 3.8 23.2 - - + +
115G HIS* 3.5 36.8 - - + +
131G ILE* 4.5 7.9 - - + -
133G LEU* 4.7 4.7 - - + -
144G VAL* 3.0 21.9 + - + +
145G ALA 3.2 8.3 - - - +
147G ASP* 1.3 77.2 - - - +
149G ARG* 1.3 61.6 + - - +
150G ALA 3.2 0.5 + - - -
151G TYR* 3.5 18.4 + - + +
162G VAL* 3.8 18.7 - - + +
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Residues in contact with ARG 149 (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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2744A G 5.9 1.0 + - - -
87G LEU* 5.0 0.2 - - + -
145G ALA 3.0 8.9 + - - +
146G ALA* 3.0 9.2 + - - +
148G LEU* 1.3 76.0 - - - +
150G ALA* 1.3 61.9 + - - +
151G TYR 3.3 0.2 - - - -
152G ARG 3.2 18.1 - - - +
153G ARG* 3.3 39.7 - - - +
154G PRO* 3.5 24.5 + - + +
162G VAL* 3.2 29.3 - - + +
164G TYR* 3.4 42.1 + - + +
167G GLU* 3.8 22.3 + - - -
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Residues in contact with ALA 150 (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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146G ALA 2.9 11.5 + - - +
147G ASP* 3.1 20.0 - - - +
148G LEU 3.1 0.4 - - - -
149G ARG* 1.3 78.4 - - - +
151G TYR* 1.3 68.7 + - + +
152G ARG* 4.3 1.0 - - - -
153G ARG* 4.4 12.7 + - - +
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Residues in contact with TYR 151 (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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105G LEU* 3.5 27.4 - - + -
107G LEU* 3.7 16.4 - - + -
109G PHE* 3.7 22.9 - + + -
113G VAL* 3.5 28.7 - - + +
114G ASP 4.1 9.7 + - - -
115G HIS* 3.0 39.8 + + + -
147G ASP 4.1 9.4 - - - -
148G LEU* 3.5 8.2 + - + +
149G ARG 3.3 1.0 - - - -
150G ALA* 1.3 81.8 - - + +
152G ARG* 1.3 60.2 + - - +
153G ARG 4.4 0.2 + - - -
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Residues in contact with ARG 152 (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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2665A A 5.3 3.0 + - - -
2666A C 3.4 21.2 + - - -
94G TYR* 3.3 20.0 + - + +
107G LEU* 2.4 46.8 + - + +
108G GLY* 3.6 17.8 + - - -
109G PHE* 3.3 33.0 - - - -
148G LEU 4.5 1.4 + - - -
149G ARG 3.2 10.0 + - - +
151G TYR* 1.3 79.1 - - - +
153G ARG* 1.3 65.3 + - - +
154G PRO 3.7 0.2 - - - -
160G LYS* 4.9 2.2 - - + +
161G GLY* 3.9 20.9 - - - -
162G VAL* 3.2 25.0 + - + +
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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