Contacts of the helix formed by residues 139 - 156 (chain A) in PDB entry 5VXA
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 SER 139 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A THR* 4.7 1.8 - - - -
137A GLY 4.0 1.4 + - - -
138A TRP* 1.3 76.9 - - - +
140A GLU* 1.3 63.4 + - - +
141A HIS* 2.9 36.3 + - - -
142A ARG* 3.1 24.3 + - - +
143A VAL* 3.3 14.0 + - - +
202A NDP 3.8 2.8 + - - -
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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
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134A THR* 5.2 5.5 - - - +
139A SER* 1.3 74.2 - - - +
141A HIS* 1.3 59.8 + - - +
143A VAL* 3.4 11.4 + - - +
144A GLN* 3.2 19.1 + - - +
175A ARG* 4.9 2.9 + - - -
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Residues in contact with HIS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A SER* 2.9 27.4 + - - -
140A GLU* 1.3 76.6 - - - +
142A ARG* 1.3 63.9 + - - +
144A GLN* 3.3 8.5 + - + +
145A GLU* 3.1 37.8 + - + +
202A NDP 3.1 29.1 + - - -
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Residues in contact with ARG 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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25A LYS* 5.5 0.8 - - - +
137A GLY 4.5 6.9 + - - -
138A TRP* 3.4 58.5 - - + +
139A SER* 3.1 20.1 + - - +
141A HIS* 1.3 75.9 - - - +
143A VAL* 1.3 65.6 + - - +
145A GLU* 3.4 3.2 + - - +
146A TYR* 3.0 21.7 + - - +
202A NDP 3.5 102.8 + - + +
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Residues in contact with VAL 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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130A LEU* 4.1 16.4 - - + +
134A THR* 3.9 26.0 - - + +
135A PRO* 4.4 5.6 - - + -
138A TRP* 3.8 22.9 - - + -
139A SER 3.3 13.1 + - - +
140A GLU* 3.5 9.6 - - - +
141A HIS 3.3 0.2 - - - -
142A ARG* 1.3 77.2 - - - +
144A GLN* 1.3 63.5 + - - +
146A TYR* 3.2 4.7 + - - +
147A PHE* 3.1 31.2 + - + -
175A ARG* 3.6 31.0 - - - +
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Residues in contact with GLN 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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140A GLU 3.2 9.9 + - - +
141A HIS* 3.3 12.5 + - + +
143A VAL* 1.3 78.1 - - - +
145A GLU* 1.3 58.3 - - + +
147A PHE* 3.1 9.6 + - - +
148A GLU* 2.9 47.1 + - - +
175A ARG* 3.1 62.2 + - - +
177A LEU* 4.1 10.7 - - - +
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Residues in contact with GLU 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 HIS* 3.1 23.9 + - + +
142A ARG* 3.7 3.8 - - + +
143A VAL 3.2 0.2 - - - -
144A GLN* 1.3 73.8 - - + +
146A TYR* 1.3 66.9 + - - +
148A GLU* 3.1 21.7 + - - +
149A TRP* 2.9 25.3 + - - +
202A NDP 2.4 43.2 + - + -
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Residues in contact with TYR 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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101A LYS* 3.9 17.5 - - - +
123A LYS* 4.6 7.6 + - + +
126A ASN* 3.5 23.7 + - + +
127A LEU* 3.6 21.8 - - + -
130A LEU* 3.3 26.2 - - + -
138A TRP* 4.1 18.4 - + + -
142A ARG 3.0 14.3 + - - +
143A VAL 3.4 9.6 - - - +
145A GLU* 1.3 75.7 - - - +
147A PHE* 1.3 56.5 + - - +
149A TRP* 3.2 31.5 + + - +
150A ALA* 2.8 31.7 + - + +
202A NDP 2.8 46.7 + - - -
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Residues in contact with PHE 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 LEU* 3.6 52.5 - - + -
130A LEU* 4.2 9.9 - - + -
131A ASN* 3.4 27.6 - - - -
143A VAL* 3.1 33.2 + - + -
144A GLN* 3.1 9.9 + - - +
146A TYR* 1.3 75.4 - - - +
148A GLU* 1.3 57.4 + - - +
150A ALA* 4.3 0.2 - - - -
151A ALA* 2.9 26.9 + - - +
171A LEU* 4.3 15.9 - - + -
172A PHE* 3.3 25.1 - + - -
175A ARG* 3.3 36.3 - - + -
177A LEU* 3.7 13.2 - - + +
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Residues in contact with GLU 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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144A GLN* 2.9 39.2 + - - +
145A GLU* 3.1 23.2 + - - +
147A PHE* 1.3 76.6 - - - +
149A TRP* 1.3 61.6 + - - +
151A ALA* 3.6 3.7 + - - +
152A GLN* 3.5 23.6 + - - +
177A LEU* 3.9 28.5 - - + +
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Residues in contact with TRP 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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101A LYS* 2.9 68.9 + - + +
104A GLN* 3.5 32.8 - - + -
105A VAL* 4.0 10.1 - - + -
123A LYS* 3.6 23.6 - - - -
145A GLU 2.9 16.0 + - - +
146A TYR* 3.6 41.3 - + - +
148A GLU* 1.3 74.6 - - - +
150A ALA* 1.3 75.6 + - - +
152A GLN* 3.0 18.2 + - + +
153A VAL* 3.1 21.8 + - + +
202A NDP 4.8 4.3 - - - -
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Residues in contact with ALA 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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123A LYS* 3.7 28.3 - - + +
127A LEU* 4.1 16.6 - - + -
146A TYR* 2.8 24.5 + - + +
147A PHE 3.8 3.4 - - - +
149A TRP* 1.3 78.6 - - + +
151A ALA* 1.3 57.6 + - - +
153A VAL* 3.1 2.5 + - - +
154A VAL* 2.9 33.4 + - - +
172A PHE* 3.7 13.2 - - + -
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Residues in contact with ALA 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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147A PHE 2.9 17.6 + - - +
148A GLU* 3.7 7.9 - - - +
149A TRP 3.2 0.2 - - - -
150A ALA* 1.3 76.9 - - - +
152A GLN* 1.3 64.2 + - - +
155A LYS* 3.0 29.6 + - - +
172A PHE* 3.4 29.3 - - + -
177A LEU* 4.7 12.3 - - + -
178A THR 5.1 2.9 - - - +
179A ILE* 3.8 13.9 - - - +
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Residues in contact with GLN 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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105A VAL* 3.9 33.1 - - + +
148A GLU 3.5 14.5 + - - +
149A TRP* 3.0 12.1 + - + +
151A ALA* 1.3 85.3 - - - +
153A VAL* 1.3 61.4 + - - +
155A LYS* 3.6 17.8 - - - +
156A GLY* 3.9 2.9 + - - -
179A ILE* 5.8 1.4 + - - -
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Residues in contact with VAL 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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104A GLN* 3.9 29.8 - - + +
105A VAL* 3.7 26.5 - - + +
108A ALA* 3.5 6.0 - - + +
119A LYS* 5.7 5.8 - - + -
123A LYS* 4.1 18.4 - - + +
149A TRP* 3.1 30.4 + - + +
150A ALA 3.1 7.2 + - - +
152A GLN* 1.3 75.5 - - - +
154A VAL* 1.3 65.3 + - - +
156A GLY* 3.0 14.7 + - - -
157A LEU* 3.5 24.5 - - + +
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Residues in contact with VAL 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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120A LEU* 4.0 9.4 - - + -
123A LYS* 4.2 23.1 - - + -
150A ALA 2.9 20.8 + - - +
151A ALA 4.1 1.3 - - - +
153A VAL* 1.3 71.5 - - - +
155A LYS* 1.3 57.9 + - - +
157A LEU* 2.7 36.1 + - + -
158A GLN* 3.6 12.9 + - + +
165A GLU* 5.4 4.3 - - + -
168A LEU* 4.0 30.7 - - + -
172A PHE* 4.1 25.8 - - + -
179A ILE 4.5 6.3 - - - +
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Residues in contact with LYS 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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151A ALA 3.0 17.9 + - - +
152A GLN* 3.6 16.4 - - - +
153A VAL 3.2 0.2 - - - -
154A VAL* 1.3 77.1 - - - +
156A GLY* 1.3 58.9 + - - +
157A LEU 3.3 0.9 + - - -
158A GLN* 3.1 31.7 + - - +
179A ILE* 4.0 21.2 + - + +
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Residues in contact with GLY 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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105A VAL 5.6 0.9 - - - -
108A ALA* 3.5 12.4 - - - +
109A PRO* 3.2 36.3 - - - +
116A LYS* 4.2 5.4 + - - -
152A GLN 3.9 2.8 + - - -
153A VAL 3.0 11.0 + - - -
155A LYS* 1.3 77.7 - - - +
157A LEU* 1.3 59.7 + - - +
158A GLN 3.6 1.5 - - - +
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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