Contacts of the helix formed by residues 161 - 175 (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 ASN 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ALA* 3.1 37.6 + - - +
49A ILE* 4.1 9.9 - - - +
117A LEU* 3.7 14.8 - - + +
120A LEU* 4.7 2.0 - - + -
159A GLY 3.9 0.4 - - - -
160A THR* 1.3 77.5 + - - +
162A ARG* 1.3 64.8 + - - +
163A GLN* 3.0 21.2 + - - +
164A LEU* 2.9 35.6 + - + +
165A GLU* 2.9 36.9 + - - +
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Residues in contact with ARG 162 (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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161A ASN* 1.3 73.3 + - - +
163A GLN* 1.3 67.7 + - + +
165A GLU* 4.1 6.0 - - - +
166A GLU* 2.8 35.6 + - + +
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Residues in contact with GLN 163 (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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46A GLU* 3.2 28.6 + - + +
47A ALA 3.6 19.5 + - - -
48A GLY* 4.6 2.8 - - - +
161A ASN* 3.0 14.4 + - - +
162A ARG* 1.3 88.7 + - + +
164A LEU* 1.3 63.4 + - - +
166A GLU* 3.9 3.6 - - - +
167A ALA* 3.1 22.9 + - - +
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Residues in contact with LEU 164 (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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42A ILE* 3.4 32.5 - - + +
43A LEU* 4.0 17.0 - - + -
46A GLU* 4.5 7.4 - - + -
47A ALA* 3.8 23.8 - - + -
117A LEU* 4.1 12.8 - - + +
120A LEU* 3.9 31.2 - - + -
121A ALA* 4.2 3.8 - - - +
124A LEU* 3.9 10.9 - - + +
161A ASN* 2.9 21.8 + - + +
163A GLN* 1.3 75.9 - - - +
165A GLU* 1.3 58.8 + - - +
167A ALA* 3.2 6.3 + - - +
168A LEU* 2.9 35.7 + - + +
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Residues in contact with GLU 165 (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* 3.8 19.2 - - + +
154A VAL* 5.4 3.5 - - + +
157A LEU 3.5 5.2 - - - +
158A GLN* 3.3 27.7 - - + +
159A GLY* 3.1 16.3 + - - -
160A THR* 2.9 13.0 + - - -
161A ASN 2.9 39.2 + - - +
162A ARG* 4.1 4.8 - - - +
164A LEU* 1.3 75.5 - - - +
166A GLU* 1.3 58.1 + - - +
168A LEU* 3.3 7.6 + - - +
169A LYS* 2.8 31.1 + - - +
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Residues in contact with GLU 166 (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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162A ARG* 2.8 25.7 + - + +
163A GLN* 3.9 4.9 - - - +
165A GLU* 1.3 77.5 - - - +
167A ALA* 1.3 61.7 + - - +
169A LYS* 3.3 7.3 + - - +
170A HIS* 3.1 22.9 + - - +
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Residues in contact with ALA 167 (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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46A GLU* 4.6 4.0 - - - +
124A LEU* 4.1 25.6 - - + -
128A ARG* 4.3 10.3 - - - +
163A GLN 3.1 15.0 + - - +
164A LEU* 3.2 7.4 + - - +
166A GLU* 1.3 75.2 - - - +
168A LEU* 1.3 62.3 + - - +
170A HIS* 3.3 8.1 + - - +
171A LEU* 3.2 25.3 + - - +
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Residues in contact with LEU 168 (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* 3.7 44.4 - - + +
123A LYS* 4.2 5.4 - - + -
124A LEU* 3.8 37.5 - - + +
127A LEU* 3.8 24.0 - - + -
154A VAL* 4.0 13.7 - - + -
164A LEU* 2.9 23.2 + - + +
165A GLU* 3.8 4.9 - - - +
167A ALA* 1.3 72.5 - - - +
169A LYS* 1.3 66.8 + - - +
171A LEU* 3.1 6.1 + - + +
172A PHE* 2.9 41.8 + - + -
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Residues in contact with LYS 169 (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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165A GLU 2.8 18.6 + - - +
166A GLU* 3.7 8.1 - - - +
168A LEU* 1.3 75.1 - - - +
170A HIS* 1.3 57.3 + - - +
172A PHE* 3.4 9.2 + - - +
173A LYS* 2.8 32.3 + - - +
177A LEU 4.8 0.2 - - - +
179A ILE* 5.6 11.7 - - - +
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Residues in contact with HIS 170 (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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166A GLU 3.1 12.9 + - - +
167A ALA* 3.6 11.2 - - - +
168A LEU 3.2 0.2 - - - -
169A LYS* 1.3 77.2 - - - +
171A LEU* 1.3 74.1 + - + +
173A LYS* 3.4 5.7 + - - +
174A GLN* 2.6 57.4 + - + +
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Residues in contact with LEU 171 (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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124A LEU* 3.8 27.4 - - + -
127A LEU* 4.1 24.0 - - + -
128A ARG* 4.0 22.0 - - + +
131A ASN* 3.8 19.2 + - - +
147A PHE* 4.3 16.3 - - + -
167A ALA 3.2 8.9 + - - +
168A LEU* 3.1 7.7 + - - +
170A HIS* 1.3 85.9 - - + +
172A PHE* 1.3 65.2 + - - +
174A GLN* 3.3 25.9 + - - +
175A ARG* 3.5 11.4 + - - +
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Residues in contact with PHE 172 (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 28.9 - - + -
147A PHE* 3.3 38.1 - + - -
150A ALA* 3.7 7.0 - - + -
151A ALA* 3.4 31.0 - - + -
154A VAL* 4.1 16.2 - - + -
168A LEU* 2.9 42.7 + - + +
169A LYS* 3.8 6.7 - - - +
171A LEU* 1.3 76.1 - - - +
173A LYS* 1.3 62.4 + - - +
175A ARG* 3.0 9.7 + - - +
176A GLY 3.2 0.2 + - - -
177A LEU* 2.8 43.5 + - + +
179A ILE 3.9 18.2 - - - +
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Residues in contact with LYS 173 (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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169A LYS 2.8 18.8 + - - +
170A HIS* 3.8 7.0 - - - +
172A PHE* 1.3 76.4 - - - +
174A GLN* 1.3 59.0 + - - +
176A GLY* 2.9 19.6 + - - -
177A LEU 3.2 12.0 + - - +
178A THR* 5.7 5.8 - - + -
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Residues in contact with GLN 174 (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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131A ASN* 4.8 8.5 - - - +
170A HIS* 2.6 51.5 + - + +
171A LEU* 3.5 23.1 + - - +
172A PHE 3.2 0.4 - - - -
173A LYS* 1.3 75.8 - - - +
175A ARG* 1.3 64.1 + - + +
176A GLY 3.5 0.4 + - - -
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Residues in contact with ARG 175 (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 4.8 0.8 + - - -
131A ASN* 2.7 36.0 + - - +
140A GLU 4.9 2.6 + - - -
143A VAL* 3.6 25.4 - - - +
144A GLN* 3.1 51.2 + - - +
147A PHE* 3.3 36.4 - - + -
171A LEU 3.5 5.0 + - - +
172A PHE 3.0 8.1 + - - +
174A GLN* 1.3 81.3 - - + +
176A GLY* 1.3 60.5 + - - +
177A LEU* 3.4 8.5 + - + +
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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