Contacts of the helix formed by residues 137 - 159 (chain A) in PDB entry 3A98
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 PRO 137 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A THR 3.7 7.0 - - - +
136A LEU* 1.3 88.9 - - + +
138A LYS* 1.3 66.9 + - - +
139A ASP* 3.4 4.7 - - + +
140A GLU* 3.3 31.4 + - + +
141A LEU* 3.0 17.5 + - - +
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Residues in contact with LYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU 3.7 1.2 + - - -
137A PRO* 1.3 71.4 - - - +
139A ASP* 1.3 75.7 + - - +
141A LEU* 3.4 11.3 + - - +
142A LYS* 3.2 25.9 + - + +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PRO* 3.4 3.3 - - + +
138A LYS* 1.3 88.3 - - - +
140A GLU* 1.3 63.4 + - - +
142A LYS* 3.2 9.0 + - - +
143A GLU* 3.2 24.9 + - - +
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A GLN* 4.8 5.4 - - - +
136A LEU* 4.0 22.5 - - + +
137A PRO* 3.3 34.0 + - + +
139A ASP* 1.3 77.7 - - - +
141A LEU* 1.3 58.3 + - - +
143A GLU* 3.1 9.8 + - + +
144A LEU* 2.8 28.5 + - + +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 3.8 29.4 - - + +
130A GLN 5.4 0.4 - - - +
131A LEU* 3.6 38.6 - - + +
136A LEU* 4.2 31.6 - - + +
137A PRO 3.0 17.4 + - - +
138A LYS* 3.5 9.9 - - - +
139A ASP 3.3 0.2 - - - -
140A GLU* 1.3 77.8 - - - +
142A LYS* 1.3 56.6 + - - +
144A LEU* 3.2 2.7 + - - +
145A LYS* 2.9 46.7 + - - +
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Residues in contact with LYS 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A LYS* 3.2 14.7 + - + +
139A ASP* 3.5 11.9 - - - +
140A GLU 3.2 0.2 - - - -
141A LEU* 1.3 80.4 - - - +
143A GLU* 1.3 62.9 + - + +
145A LYS* 3.4 14.2 + - + +
146A GLN* 3.3 40.4 + - - +
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Residues in contact with GLU 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASP 3.2 11.6 + - - +
140A GLU* 3.1 11.7 + - + +
142A LYS* 1.3 78.7 - - + +
144A LEU* 1.3 63.5 + - - +
146A GLN* 3.3 25.9 + - - +
147A LYS* 3.1 34.8 + - - +
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Residues in contact with LEU 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TRP* 3.8 40.4 - - + +
130A GLN* 3.8 25.6 - - + +
131A LEU* 3.7 24.0 - - + +
136A LEU* 3.5 27.6 - - + -
140A GLU* 2.8 14.7 + - + +
141A LEU 3.5 8.1 - - - +
143A GLU* 1.3 77.2 - - - +
145A LYS* 1.3 63.1 + - - +
147A LYS* 3.1 17.6 + - + +
148A VAL* 3.0 22.1 + - + +
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Residues in contact with LYS 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ALA* 3.4 21.6 - - + +
84A GLU* 3.1 39.7 + - - +
87A LEU* 4.0 19.7 - - + -
131A LEU* 4.0 13.2 - - + -
141A LEU* 2.9 36.8 + - - +
142A LYS* 3.7 13.9 - - + +
143A GLU 3.3 0.2 - - - -
144A LEU* 1.3 76.4 - - - +
146A GLN* 1.3 57.9 + - + +
148A VAL* 3.3 3.6 + - - +
149A THR* 3.0 35.4 + - + +
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LYS* 3.3 33.0 + - - +
143A GLU* 3.3 27.9 + - - +
144A LEU 3.1 0.6 - - - -
145A LYS* 1.3 77.9 - - + +
147A LYS* 1.3 61.4 + - - +
149A THR* 3.1 7.6 + - - +
150A SER* 2.6 36.7 + - - +
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Residues in contact with LYS 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A TRP* 3.6 38.1 - - + -
143A GLU* 3.1 27.2 + - - +
144A LEU* 3.1 21.6 + - + +
146A GLN* 1.3 75.1 - - - +
148A VAL* 1.3 61.6 + - - +
150A SER* 3.5 5.2 + - - -
151A LYS* 3.1 18.7 + - - +
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Residues in contact with VAL 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.8 23.1 - - + -
91A VAL* 3.7 28.9 - - + -
124A LEU* 4.0 5.5 - - + +
127A TRP* 3.7 37.2 - - + -
128A ARG 5.2 0.7 - - - +
131A LEU* 3.9 16.4 - - + -
144A LEU* 3.0 18.4 + - + +
145A LYS 3.5 7.6 - - - +
147A LYS* 1.3 74.9 - - - +
149A THR* 1.3 66.0 + - - +
151A LYS* 3.3 3.3 + - - +
152A ILE* 3.0 27.4 + - + +
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Residues in contact with THR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.0 23.1 - - + -
90A GLU* 5.6 1.6 - - - +
145A LYS* 3.0 19.2 + - + +
146A GLN* 3.1 15.1 + - - +
148A VAL* 1.3 76.4 - - - +
150A SER* 1.3 60.6 + - - +
152A ILE* 3.8 6.9 - - + +
153A ASP* 3.0 43.0 + - - +
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Residues in contact with SER 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A GLN* 2.6 25.6 + - - +
147A LYS* 3.8 6.2 - - - -
148A VAL 3.2 0.2 - - - -
149A THR* 1.3 80.7 + - - +
151A LYS* 1.3 57.9 + - - +
153A ASP* 3.9 4.5 - - - +
154A TYR* 2.9 31.1 + - - +
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Residues in contact with LYS 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TRP* 3.4 2.9 - - + -
119A SER 5.8 0.2 - - - -
120A MSE 3.1 68.6 - - + +
123A ASP* 3.6 16.8 + - + -
124A LEU* 4.1 12.8 - - + -
127A TRP* 3.4 33.4 - - + -
147A LYS 3.1 16.3 + - - +
148A VAL 3.3 2.9 + - - +
150A SER* 1.3 74.4 - - - +
152A ILE* 1.3 61.0 + - - +
154A TYR* 4.6 1.8 - - - -
155A GLY 2.8 26.3 + - - -
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Residues in contact with ILE 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.4 5.4 - - + -
90A GLU* 3.5 38.4 - - + +
91A VAL* 4.0 14.6 - - + -
94A THR* 3.8 17.5 - - + +
98A TRP* 3.4 9.4 - - - -
124A LEU* 4.1 18.8 - - + -
148A VAL* 3.0 37.3 + - + +
149A THR* 3.8 6.1 - - - +
151A LYS* 1.3 76.7 - - - +
153A ASP* 1.3 63.0 + - - +
156A ASN* 2.8 47.6 + - - +
164A ILE* 4.9 0.4 - - + -
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Residues in contact with ASP 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLU* 5.0 0.5 - - - +
149A THR* 3.0 29.3 + - - +
150A SER* 3.9 5.5 - - - +
152A ILE* 1.3 82.2 - - - +
154A TYR* 1.3 62.4 + - - +
156A ASN* 3.7 5.5 + - - +
157A LYS* 3.0 23.2 + - - +
164A ILE* 4.0 32.1 + - - +
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Residues in contact with TYR 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 5.5 1.4 + - - -
116A GLN* 3.7 27.2 + - - -
120A MSE 3.9 17.9 - - + -
150A SER 2.9 22.0 + - - +
151A LYS* 4.0 3.4 - - - +
153A ASP* 1.3 72.0 - - - +
155A GLY* 1.3 64.5 + - - +
157A LYS* 3.0 27.9 + - + +
158A ILE* 3.0 39.7 + - + +
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Residues in contact with GLY 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TRP* 3.4 22.9 - - - -
120A MSE 3.4 20.7 - - - +
151A LYS 2.8 14.8 + - - -
154A TYR* 1.3 73.9 - - - +
156A ASN* 1.3 61.3 + - - +
158A ILE* 3.4 5.5 + - - +
159A LEU* 3.1 30.6 + - - +
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Residues in contact with ASN 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 4.4 6.3 + - - +
97A GLU* 5.5 2.1 - - - +
98A TRP* 2.9 23.7 + - - +
152A ILE* 2.8 40.2 + - - +
153A ASP* 3.7 6.4 - - - +
155A GLY* 1.3 73.5 - - - +
157A LYS* 1.3 59.4 + - - +
160A GLU 3.1 3.1 + - - -
161A LEU* 2.6 49.9 + - + +
162A ASP 3.6 24.7 + - - +
163A LEU* 5.3 3.8 - - + -
164A ILE* 3.9 15.1 - - - +
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Residues in contact with LYS 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A ASP 3.0 13.1 + - - +
154A TYR* 3.0 25.4 + - + +
156A ASN* 1.3 78.1 - - - +
158A ILE* 1.3 61.6 + - + +
160A GLU* 3.0 22.2 + - - +
161A LEU 5.2 1.1 - - - -
163A LEU* 5.7 14.4 - - + -
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ARG* 3.0 34.4 + - - +
116A GLN* 3.3 38.6 - - + +
117A VAL* 5.1 3.8 - - + -
120A MSE 4.5 10.8 - - - -
154A TYR* 3.0 48.0 + - + +
155A GLY 3.5 9.9 - - - +
157A LYS* 1.3 79.1 - - + +
159A LEU* 1.3 73.4 + - + +
160A GLU* 3.1 7.5 + - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A TRP* 3.6 47.3 - - + +
101A ILE* 4.0 34.7 - - + +
105A LEU* 4.6 6.1 - - + -
113A ARG* 5.0 7.0 - - + -
117A VAL* 4.0 28.9 - - + -
155A GLY* 3.1 17.4 + - - +
158A ILE* 1.3 87.9 - - + +
160A GLU* 1.3 73.9 + - - +
161A LEU* 3.5 18.0 + - + +
620D LYS* 5.2 1.7 + - - -
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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
------------------------------------------------------------
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