Contacts of the helix formed by residues 136 - 151 (chain A) in PDB entry 5IYB
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 GLN 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A SER* 2.4 58.5 + - - +
135A GLY* 1.3 70.6 + - - +
137A PRO* 1.3 69.4 - - - +
138A LYS* 3.4 24.5 + - - +
139A LYS* 3.7 27.4 - - + +
140A ARG* 3.4 14.8 + - - +
1423A ASP* 3.6 34.4 + - - +
1445A HIS* 4.1 2.9 - - - -
1447A GLU* 5.1 2.8 - - - +
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Residues in contact with PRO 137 (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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133A SER 4.2 0.4 - - - -
134A LYS 4.7 4.9 - - - +
135A GLY 3.2 13.7 - - - +
136A GLN* 1.3 89.1 - - - +
138A LYS* 1.3 55.2 + - - +
140A ARG* 3.1 19.3 - - + +
141A LEU* 2.9 27.5 + - - +
237A GLY* 3.4 32.4 - - - +
1445A HIS* 3.0 29.8 - - + +
1447A GLU* 5.1 3.6 - - - +
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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
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136A GLN* 3.2 14.5 + - - +
137A PRO* 1.3 73.2 - - - +
139A LYS* 1.3 66.2 + - - +
141A LEU* 3.1 10.2 + - + +
142A THR* 3.0 34.1 + - + +
1420A ASN 5.9 0.4 + - - -
1421A ARG* 5.4 12.9 - - - +
1429A LYS* 5.9 3.6 - - - +
1441A GLU* 2.4 42.4 + - + +
1445A HIS* 2.9 30.4 - - + +
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Residues in contact with LYS 139 (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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132A LYS* 4.8 11.7 - - + +
133A SER* 4.3 10.5 - - - +
136A GLN* 3.6 24.5 + - + +
137A PRO 3.5 0.2 - - - -
138A LYS* 1.3 78.6 - - - +
140A ARG* 1.3 57.5 + - - +
142A THR* 2.8 21.9 + - - +
143A HIS* 2.9 52.6 + - + +
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Residues in contact with ARG 140 (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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129A ILE* 3.6 28.4 + - + +
130A LEU* 4.2 26.8 + - + +
132A LYS 5.5 1.1 + - - -
133A SER* 4.1 6.4 + - - -
134A LYS* 3.6 38.4 + - - +
136A GLN 3.4 6.8 + - - +
137A PRO* 3.1 24.5 + - - +
139A LYS* 1.3 79.0 - - - +
141A LEU* 1.3 53.6 + - - +
143A HIS* 3.3 1.4 + - - +
144A VAL* 2.8 37.8 + - + +
234A PHE* 2.7 63.1 + - - -
235A VAL* 3.1 24.5 - - - +
237A GLY* 4.6 6.2 - - - +
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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
----------------------------------------------------------
102A LYS* 5.5 11.9 - - + +
105A LYS* 5.4 16.6 - - + +
106A VAL* 5.0 14.6 - - + -
109A CYS* 4.7 8.5 - - - -
137A PRO 2.9 15.2 + - - +
138A LYS* 3.1 13.0 + - + +
140A ARG* 1.3 72.8 - - - +
142A THR* 1.3 62.3 + - + +
144A VAL* 3.8 3.9 - - + -
145A TYR* 2.8 32.9 + - + +
236A LEU* 3.7 44.6 + - + +
238A MET* 5.6 5.4 - - + -
1445A HIS* 5.9 5.6 - - + +
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Residues in contact with THR 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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105A LYS* 5.3 11.4 - - - +
138A LYS* 3.0 27.9 + - + +
139A LYS* 2.8 27.5 + - - +
141A LEU* 1.3 78.6 - - + +
143A HIS* 1.3 64.2 + - - +
145A TYR* 3.5 8.8 + - - +
146A ASP* 3.0 28.8 + - - +
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Residues in contact with HIS 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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129A ILE* 4.2 31.9 - - + +
132A LYS* 5.4 16.4 + - + +
139A LYS* 2.9 50.0 + - + +
140A ARG 3.8 3.1 - - - +
142A THR* 1.3 82.6 + - - +
144A VAL* 1.3 61.1 + - - +
146A ASP* 3.5 5.9 + - + +
147A LEU* 3.0 29.3 + - - +
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Residues in contact with VAL 144 (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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109A CYS* 3.7 14.6 - - + -
117A LEU* 4.5 11.2 - - + -
119A VAL* 5.8 0.9 - - + -
126A ILE* 4.6 15.5 - - + -
129A ILE* 4.7 6.5 - - + -
130A LEU* 6.5 0.2 - - + -
140A ARG* 2.8 30.4 + - + +
141A LEU* 3.8 5.8 - - - +
143A HIS* 1.3 68.9 - - - +
145A TYR* 1.3 57.6 + - - +
147A LEU* 3.3 5.2 + - - +
148A CYS* 2.8 51.6 + - - -
235A VAL* 4.1 26.2 - - + +
236A LEU* 4.4 11.2 - - + -
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Residues in contact with TYR 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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105A LYS* 3.6 55.7 - - + +
108A ARG* 2.4 56.5 + - + -
109A CYS* 3.5 11.9 - - - -
141A LEU* 2.8 20.8 + - + +
142A THR* 3.6 8.3 - - - +
144A VAL* 1.3 76.5 - - - +
146A ASP* 1.3 61.7 + - + +
148A CYS* 3.3 1.6 + - - +
149A LYS* 2.9 53.2 + - + +
49X T 4.9 16.8 + - - -
50X C 4.4 1.9 + - - -
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Residues in contact with ASP 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 THR 3.0 16.9 + - - +
143A HIS* 3.8 7.2 - - + +
145A TYR* 1.3 82.7 - - + +
147A LEU* 1.3 60.3 + - - +
149A LYS* 3.3 29.9 + - - +
150A GLY* 3.3 16.3 + - - -
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Residues in contact with LEU 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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119A VAL* 4.0 6.1 - - + -
123A ASN* 5.2 4.3 - - - +
125A LYS* 5.2 19.1 - - + -
126A ILE* 3.7 33.2 - - + -
129A ILE* 4.5 8.1 - - + -
143A HIS 3.0 17.4 + - - +
144A VAL* 3.7 4.5 - - - +
146A ASP* 1.3 77.0 + - - +
148A CYS* 1.3 59.4 + - - +
150A GLY* 3.3 3.6 + - - -
151A LYS* 3.0 62.8 + - + +
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Residues in contact with CYS 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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108A ARG 3.9 4.9 - - - +
109A CYS* 3.7 34.8 - - - +
117A LEU* 3.8 14.1 - - - -
118A LEU* 3.3 24.2 - - + +
119A VAL* 4.7 6.3 - - - -
144A VAL* 2.8 43.7 + - - +
145A TYR 3.8 3.4 - - - +
147A LEU* 1.3 71.7 - - - +
149A LYS* 1.3 61.4 + - - +
151A LYS* 2.9 27.9 - - - +
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Residues in contact with LYS 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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108A ARG* 5.7 9.6 - - + +
145A TYR* 2.9 39.6 + - + +
146A ASP* 3.3 31.0 + - - +
148A CYS* 1.3 76.0 - - - +
150A GLY* 1.3 61.3 + - - +
151A LYS 4.5 1.7 - - - +
152A ASN* 5.1 4.3 - - - +
50X C 5.9 3.8 - - - +
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Residues in contact with GLY 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 ASP 3.3 7.6 + - - -
147A LEU* 3.3 7.5 + - - -
148A CYS 3.2 0.4 - - - -
149A LYS* 1.3 81.7 - - - +
151A LYS* 1.3 60.2 + - - +
152A ASN* 3.4 6.9 + - - +
39Y G 5.6 5.3 + - - -
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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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118A LEU* 3.5 31.3 - - + +
119A VAL* 3.6 39.7 - - + +
123A ASN* 4.1 14.3 - - - +
147A LEU* 3.0 48.6 + - + +
148A CYS* 2.9 24.3 + - - +
149A LYS 4.5 0.2 - - - +
150A GLY* 1.3 74.5 - - - +
152A ASN* 1.3 63.0 + - - +
153A ILE 4.2 0.4 - - - -
188A GLN* 5.3 0.7 - - - +
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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
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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