Contacts of the helix formed by residues 136 - 153 (chain A) in PDB entry 5E2Q
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 HIS 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.7 21.4 + - - +
132A ALA 3.1 10.4 + - - +
133A ALA 3.5 3.1 - - - -
135A GLN* 1.3 102.2 + - + +
137A PRO* 1.3 66.2 - - - +
138A GLU 3.3 3.3 + - - -
139A GLU* 3.3 31.5 + - + +
140A VAL* 3.2 24.0 + - + +
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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 ALA* 3.1 20.8 - - + +
134A GLN* 3.8 7.2 - - - +
135A GLN 3.7 6.1 - - - +
136A HIS* 1.3 88.3 - - - +
138A GLU* 1.3 85.4 + - - +
140A VAL* 4.8 0.4 - - + -
141A ARG* 3.1 39.8 + - + +
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Residues in contact with GLU 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 HIS 3.3 0.8 - - - -
137A PRO* 1.3 98.9 - - - +
139A GLU* 1.3 70.6 + - - +
141A ARG* 3.8 3.1 - - - +
142A GLY* 2.8 27.0 + - - -
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Residues in contact with GLU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ARG* 3.5 31.5 + - - +
136A HIS* 3.3 45.9 - - + +
138A GLU* 1.3 87.9 - - - +
140A VAL* 1.3 59.0 + - - +
142A GLY* 3.8 2.4 - - - +
143A LEU* 2.9 38.5 + - + +
713A GLU* 5.6 1.4 - - - +
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Residues in contact with VAL 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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62A LEU* 4.3 9.4 - - + +
65A ARG* 4.4 17.9 - - + -
66A LEU* 5.5 0.9 - - + -
127A ILE* 3.8 27.1 - - + +
128A LEU* 4.7 4.5 - - + -
130A SER* 4.9 0.7 - - - +
132A ALA* 3.4 26.2 - - + +
133A ALA* 3.7 24.7 - - + +
136A HIS* 3.2 20.3 + - + +
137A PRO 4.2 1.8 - - - +
139A GLU* 1.3 75.7 - - - +
141A ARG* 1.3 61.7 + - + +
143A LEU* 3.3 6.2 + - - +
144A TRP* 3.0 28.9 + - - +
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Residues in contact with ARG 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.7 46.7 - - + +
133A ALA* 6.2 1.3 - - + -
137A PRO* 3.1 29.4 + - + +
138A GLU* 4.0 3.1 - - - +
140A VAL* 1.3 76.4 - - + +
142A GLY* 1.3 56.7 + - - +
144A TRP* 3.6 2.6 + - - +
145A GLN* 3.0 31.5 + - - +
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Residues in contact with GLY 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A GLU 2.8 19.4 + - - -
139A GLU* 3.9 2.2 - - - -
141A ARG* 1.3 75.0 - - - +
143A LEU* 1.3 62.6 + - - +
145A GLN* 3.4 11.9 + - - +
146A THR* 2.8 30.2 + - - -
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Residues in contact with LEU 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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58A TYR* 3.8 39.7 - - + +
61A ALA* 3.8 10.1 - - + +
62A LEU* 3.6 42.4 - - + +
65A ARG* 4.1 18.6 - - - +
139A GLU* 2.9 25.4 + - + +
140A VAL 3.8 3.4 - - - +
142A GLY* 1.3 74.2 - - - +
144A TRP* 1.3 58.9 + - - +
146A THR* 3.1 4.9 + - - -
147A CYS* 2.9 35.6 + - - -
716A THR* 4.2 17.9 - - + +
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Residues in contact with TRP 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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62A LEU* 3.9 13.4 - - + +
120A LYS* 3.6 32.4 + - + +
123A LEU* 4.3 6.5 - - + -
124A GLU* 3.3 51.3 + - + +
127A ILE* 3.5 36.8 - - + -
128A LEU* 4.6 13.9 - - + -
140A VAL 3.0 16.8 + - - +
141A ARG* 4.0 5.6 - - - +
143A LEU* 1.3 76.3 - - - +
145A GLN* 1.3 61.0 + - - +
148A GLY* 3.0 34.6 + - - +
151A MET* 3.9 22.9 - - + -
152A PHE* 3.9 22.4 - + - -
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Residues in contact with GLN 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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141A ARG 3.0 19.3 + - - +
142A GLY* 3.6 10.9 - - - +
143A LEU 3.2 0.2 - - - -
144A TRP* 1.3 81.5 - - - +
146A THR* 1.3 63.3 + - - +
148A GLY 4.5 1.4 + - - -
149A GLU* 5.1 5.5 + - - +
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Residues in contact with THR 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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55A GLU* 5.5 0.3 - - - +
58A TYR* 3.6 45.8 - - + +
142A GLY 2.8 22.0 + - - -
143A LEU* 3.1 6.0 + - - -
145A GLN* 1.3 82.6 - - - +
147A CYS* 1.3 58.6 + - - +
148A GLY 3.6 0.2 - - - -
149A GLU* 5.1 2.9 + - - +
150A LEU* 5.0 11.4 + - - +
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Residues in contact with CYS 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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55A GLU* 4.2 12.3 - - + +
58A TYR* 3.6 28.5 - - + -
59A ILE* 4.0 26.8 - - + +
62A LEU* 4.1 11.4 - - - -
143A LEU 2.9 26.6 + - - -
144A TRP* 4.6 0.2 - - - -
146A THR* 1.3 75.8 - - - +
148A GLY* 1.3 61.0 + - - +
149A GLU 3.4 2.9 - - - -
150A LEU* 3.5 4.1 + - - +
151A MET* 2.9 43.4 + - - +
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Residues in contact with GLY 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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120A LYS* 3.3 19.9 - - - -
144A TRP* 3.0 45.2 + - - -
145A GLN 4.4 0.2 - - - -
146A THR 3.6 0.4 - - - -
147A CYS* 1.3 79.6 - - - +
149A GLU* 1.3 62.4 + - - +
151A MET* 3.3 16.0 + - - +
152A PHE* 3.5 5.4 - - - -
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Residues in contact with GLU 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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120A LYS* 3.9 16.5 + - - +
145A GLN 5.1 6.0 + - - +
146A THR 5.1 2.4 + - - +
147A CYS 3.4 0.4 - - - -
148A GLY* 1.3 74.4 - - - +
150A LEU* 1.3 66.6 + - + +
151A MET 3.3 0.5 + - - -
152A PHE* 3.3 4.0 + - - +
153A SER* 3.1 36.5 + - - -
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Residues in contact with LEU 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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54A PRO* 5.0 7.9 - - + -
55A GLU* 3.4 48.2 - - + +
105A ASN* 4.3 0.3 + - - -
113A LYS* 2.7 33.5 + - - +
146A THR 5.0 8.9 + - - +
147A CYS 3.5 4.5 + - - +
148A GLY 3.4 0.4 - - - -
149A GLU* 1.3 82.8 - - + +
151A MET* 1.3 62.8 + - - +
152A PHE 3.2 0.2 - - - -
153A SER* 4.0 4.0 - - - -
157A ARG* 5.9 2.2 - - - +
158A LEU* 4.0 31.2 - - + -
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Residues in contact with MET 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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59A ILE* 4.2 26.2 - - + -
62A LEU* 4.3 10.3 - - + -
63A LEU* 5.7 4.3 - - + -
92A PHE* 5.8 1.6 - - + -
95A TYR* 3.4 24.9 + - + +
105A ASN* 5.3 0.6 + - - +
113A LYS* 4.6 1.8 - - - +
114A PHE 4.5 0.9 - - - +
115A VAL* 3.2 18.2 - - - +
116A PRO* 3.3 23.3 - - + +
123A LEU* 4.0 8.3 - - + -
127A ILE* 5.4 0.9 - - + -
144A TRP* 3.9 21.8 - - + -
147A CYS* 2.9 41.1 + - - +
148A GLY 3.4 7.9 - - - +
149A GLU 3.1 0.4 - - - -
150A LEU* 1.3 78.9 - - - +
152A PHE* 1.3 76.5 + - + +
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Residues in contact with PHE 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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115A VAL* 3.4 19.9 - - + +
116A PRO* 3.7 34.1 - - + -
118A LEU* 3.3 26.2 - - + -
120A LYS* 3.8 44.6 - - + -
123A LEU* 3.8 15.0 - - + -
144A TRP* 3.9 8.5 - + - -
148A GLY 3.5 13.9 - - - +
149A GLU 3.3 5.2 + - - +
151A MET* 1.3 102.0 - - + +
153A SER* 1.3 65.1 + - - +
154A LEU* 3.3 6.9 + - - +
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Residues in contact with SER 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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113A LYS* 2.8 35.4 + - - +
149A GLU* 3.1 27.2 + - - -
150A LEU* 3.9 6.5 + - - -
151A MET 3.7 0.8 - - - -
152A PHE* 1.3 76.0 - - - +
154A LEU* 1.3 61.7 + - - +
155A GLU* 3.5 16.2 + - - +
158A LEU* 3.3 26.7 - - - +
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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