Contacts of the helix formed by residues 131 - 154 (chain G) in PDB entry 2YW7
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 131 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LYS* 4.0 15.7 + - - +
14G ALA* 6.3 0.9 - - + -
17G VAL* 4.0 24.6 - - + +
71G ARG* 2.8 24.6 + - - -
75G LEU* 4.0 4.6 - - - +
127G LEU* 2.9 15.5 + - + +
130G LEU* 1.3 77.3 - - - +
132G LEU* 1.3 64.9 + - - +
133G VAL* 3.0 16.1 + - - +
134G SER* 2.7 26.5 + - - -
135G GLN* 3.0 17.0 + - - +
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Residues in contact with LEU 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G LEU 3.6 2.7 + - - +
128G GLU* 5.0 17.9 - - + +
130G LEU 5.6 1.3 - - - +
131G ASP* 1.3 75.1 - - - +
133G VAL* 1.3 56.9 + - + +
135G GLN* 3.3 18.1 - - - +
136G ASP* 2.7 36.3 + - - +
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Residues in contact with VAL 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G ARG* 3.3 26.2 - - - +
131G ASP* 3.0 15.0 + - - +
132G LEU* 1.3 80.2 - - + +
134G SER* 1.3 58.4 + - - +
136G ASP* 3.1 23.4 - - - +
137G LEU* 3.3 7.8 + - - +
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Residues in contact with SER 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G VAL* 4.7 2.0 - - - -
21G LEU* 3.8 25.5 - - - +
71G ARG* 2.6 35.8 + - - +
127G LEU* 3.9 9.6 - - - -
131G ASP* 2.7 20.6 + - - -
133G VAL* 1.3 72.0 - - - +
135G GLN* 1.3 58.0 + - - +
136G ASP 2.8 10.5 + - - -
137G LEU* 3.0 9.9 + - - +
138G LEU* 2.9 27.4 + - - +
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Residues in contact with GLN 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ILE* 3.2 43.4 + - + +
127G LEU* 3.4 33.9 - - + +
128G GLU* 3.7 29.6 + - - +
131G ASP 3.0 8.8 + - - +
132G LEU* 3.4 20.2 - - - +
134G SER* 1.3 76.1 - - - +
136G ASP* 1.3 55.9 + - - +
138G LEU* 4.0 4.4 - - - +
139G ILE* 2.9 38.2 + - - +
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Residues in contact with ASP 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G LEU 2.7 11.6 + - - +
133G VAL* 3.1 13.9 - - - +
134G SER 2.8 1.2 - - - -
135G GLN* 1.3 77.1 - - - +
137G LEU* 1.3 67.2 + - - +
138G LEU 3.0 1.3 - - - -
139G ILE* 2.8 27.9 + - - +
140G ALA* 2.9 13.7 + - - +
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Residues in contact with LEU 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU* 5.2 0.9 - - + -
67G GLU* 3.0 35.4 - - + +
68G VAL* 4.0 31.6 - - + +
71G ARG* 4.1 23.6 - - + -
133G VAL 3.3 7.6 + - - +
134G SER* 3.0 9.6 + - - +
136G ASP* 1.3 79.5 + - - +
138G LEU* 1.3 65.0 + - + +
140G ALA* 3.5 7.8 - - + +
141G HIS* 3.2 46.3 + - + +
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Residues in contact with LEU 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G LEU* 4.1 24.2 - - + -
24G GLN* 3.3 45.3 - - + +
28G TYR* 4.7 1.1 - - - +
68G VAL* 5.4 2.0 - - + -
120G THR* 3.6 27.2 - - + +
123G SER* 4.3 7.6 - - - -
124G ILE* 3.8 16.2 - - + +
127G LEU* 4.3 11.7 - - + -
134G SER 2.9 18.3 + - - +
135G GLN* 4.0 4.3 - - - +
137G LEU* 1.3 84.7 - - + +
139G ILE* 1.3 66.6 + - - +
141G HIS* 3.4 10.4 + - + +
142G ALA* 3.0 23.0 + - - +
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Residues in contact with ILE 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G ILE* 3.7 25.4 - - + -
135G GLN* 2.9 41.5 + - - +
136G ASP* 2.8 23.3 + - - +
138G LEU* 1.3 69.8 - - - +
140G ALA* 1.3 72.0 + - - +
142G ALA* 3.2 12.4 + - + +
143G GLY* 3.2 9.2 + - - -
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Residues in contact with ALA 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G ASP 2.9 10.1 + - - +
137G LEU* 3.5 15.5 - - + +
139G ILE* 1.3 79.7 - - - +
141G HIS* 1.3 71.1 + - + +
143G GLY* 3.1 9.4 + - - -
144G GLU* 3.3 14.9 + - - +
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Residues in contact with HIS 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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28G TYR* 2.6 42.5 + + - +
64G TYR* 3.5 48.3 - + + -
67G GLU* 3.0 23.9 + - - -
68G VAL* 5.2 1.3 - - + -
120G THR* 5.3 0.4 - - + -
137G LEU* 3.2 38.5 + - + +
138G LEU* 3.4 11.1 + - + +
139G ILE 3.3 0.2 - - - -
140G ALA* 1.3 83.2 - - + +
142G ALA* 1.3 56.5 + - - +
144G GLU* 2.7 4.7 + - - +
145G LEU* 2.7 38.9 + - + +
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Residues in contact with ALA 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ILE* 4.5 7.1 - - + +
120G THR* 3.8 21.5 - - + +
121G ARG* 5.3 4.5 - - + -
124G ILE* 4.0 10.8 - - + -
138G LEU 3.0 10.8 + - - +
139G ILE* 3.3 10.8 - - + +
141G HIS* 1.3 76.3 - - - +
143G GLY* 1.3 52.9 + - - +
145G LEU* 3.3 6.8 + - - +
146G GLU* 2.6 51.7 + - - +
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Residues in contact with GLY 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139G ILE 3.2 4.5 + - - -
140G ALA 3.1 8.1 + - - -
142G ALA* 1.3 79.4 - - - +
144G GLU* 1.3 58.1 + - - +
146G GLU* 3.4 13.2 + - - +
147G LYS* 3.0 27.4 + - - +
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Residues in contact with GLU 144 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G GLN* 4.9 2.5 - - - +
60G LEU* 4.1 16.0 - - + +
64G TYR* 2.7 28.9 - - - +
140G ALA 3.3 11.0 + - - +
141G HIS 2.7 10.2 + - - +
143G GLY* 1.3 70.3 - - - +
145G LEU* 1.3 63.0 + - - +
147G LYS* 3.3 20.3 + - - +
148G PHE* 3.1 21.0 + - - +
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Residues in contact with LEU 145 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G TYR* 4.0 19.7 - - + +
31G LEU* 4.2 13.2 - - + -
57G GLN* 4.0 13.2 - - - +
61G VAL* 4.6 1.6 - - + -
64G TYR* 4.0 16.6 - - + -
113G TYR* 3.8 25.7 - - + -
116G VAL* 4.6 13.5 - - + -
117G ILE* 3.5 23.8 - - + +
120G THR* 4.6 7.6 - - + +
141G HIS* 2.7 40.9 + - + +
142G ALA* 3.7 6.3 - - - +
144G GLU* 1.3 69.0 - - - +
146G GLU* 1.3 65.0 + - - +
148G PHE* 3.2 5.6 + - - +
149G GLN* 3.1 18.4 + - - +
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Residues in contact with GLU 146 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G ILE* 3.7 25.3 - - + +
121G ARG* 3.6 31.5 + - - +
142G ALA* 2.6 34.8 + - - +
143G GLY* 3.4 11.0 + - - +
145G LEU* 1.3 73.1 - - - +
147G LYS* 1.3 59.8 + - - +
149G GLN* 3.5 6.7 + - - +
150G TRP* 3.2 19.9 + - - +
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Residues in contact with LYS 147 (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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143G GLY 3.0 12.7 + - - +
144G GLU* 3.6 23.6 - - - +
145G LEU 3.2 0.4 - - - -
146G GLU* 1.3 75.8 - - - +
148G PHE* 1.3 66.0 + - - +
150G TRP* 3.1 29.4 + - + +
151G PHE* 3.0 29.4 + - + +
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Residues in contact with PHE 148 (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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35G LEU* 4.8 2.0 - - + -
53G MET* 3.3 41.7 - - + -
54G ILE* 4.4 16.6 - - + -
57G GLN* 3.1 40.6 - - + +
109G LEU* 4.6 7.0 - - + -
113G TYR* 3.2 43.7 - + + -
144G GLU 3.1 11.0 + - - +
145G LEU 3.2 7.1 + - - +
147G LYS* 1.3 75.6 - - - +
149G GLN* 1.3 52.5 + - - +
151G PHE* 3.3 11.4 + + + +
152G VAL* 2.8 55.4 + - + +
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Residues in contact with GLN 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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110G ASP* 2.9 26.3 - - - +
113G TYR* 3.3 9.4 - - + +
114G ASN* 3.3 23.5 + - - +
117G ILE* 3.8 24.8 - - + +
121G ARG* 5.3 7.7 - - - +
145G LEU 3.1 4.0 + - - +
146G GLU* 3.5 10.6 + - - +
148G PHE* 1.3 80.4 - - - +
150G TRP* 1.3 52.3 + - - +
152G VAL* 3.1 8.3 + - - +
153G ARG* 2.7 82.6 + - + +
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Residues in contact with TRP 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 GLU 3.2 9.7 + - - +
147G LYS* 3.1 36.0 + - + +
149G GLN* 1.3 78.2 - - - +
151G PHE* 1.3 100.5 + + + +
153G ARG* 2.8 23.2 + - + +
154G ALA* 3.2 19.1 + - + +
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Residues in contact with PHE 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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53G MET* 3.4 37.9 - - + +
147G LYS* 3.0 16.2 + - + +
148G PHE* 3.4 16.2 - + - +
150G TRP* 1.3 99.7 - + + +
152G VAL* 1.3 60.9 + - - +
154G ALA* 3.2 26.2 - - + +
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Residues in contact with VAL 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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53G MET* 3.6 17.7 - - + -
106G LEU* 3.5 37.3 - - + +
109G LEU* 4.6 8.3 - - + -
110G ASP* 3.9 20.2 - - + +
113G TYR* 6.2 0.4 - - + -
148G PHE* 2.8 55.3 + - + +
149G GLN* 3.4 6.7 - - - +
151G PHE* 1.3 70.3 - - - +
153G ARG* 1.3 63.2 + - - +
154G ALA 3.0 12.1 + - - +
155G HIS* 3.4 15.8 - - - +
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Residues in contact with ARG 153 (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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110G ASP* 2.7 28.7 + - - +
114G ASN* 3.4 24.5 + - - +
149G GLN* 2.7 55.1 + - + +
150G TRP* 2.8 12.6 + - + +
152G VAL* 1.3 72.1 - - - +
154G ALA* 1.3 55.9 + - - +
155G HIS* 2.9 23.8 + - - +
156G LEU* 5.6 1.0 - - - +
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Residues in contact with ALA 154 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G LEU* 5.1 1.6 - - - +
150G TRP* 3.2 19.6 + - + +
151G PHE* 3.2 23.4 - - + +
152G VAL 3.0 2.6 - - - +
153G ARG* 1.3 72.2 - - - +
155G HIS* 1.3 61.1 + - - +
156G LEU* 6.4 0.2 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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