Contacts of the helix formed by residues 154 - 168 (chain A) in PDB entry 1XVI
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A TRP* 3.3 5.9 + - - -
153A ASP* 1.3 82.7 + - - +
155A ASP* 1.3 60.5 + - - +
156A GLU* 3.7 7.7 + - - +
157A ARG* 3.1 27.7 + - - +
158A MET 2.9 24.1 + - - -
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Residues in contact with ASP 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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153A ASP 4.8 2.3 - - - +
154A SER* 1.3 76.1 - - - +
156A GLU* 1.3 56.6 + - - +
158A MET* 3.2 23.1 + - + +
159A ALA* 3.0 27.4 + - - +
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Residues in contact with GLU 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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154A SER* 3.3 8.1 + - - +
155A ASP* 1.3 77.4 - - - +
157A ARG* 1.3 67.6 + - + +
159A ALA* 3.4 8.4 + - - +
160A GLN* 3.3 39.1 + - - +
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Residues in contact with ARG 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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111A GLU* 2.5 31.9 + - - +
112A HIS* 3.4 20.6 + - - +
113A PHE* 3.2 32.6 - - + +
114A LYS* 6.2 0.2 - - - +
151A TRP* 3.7 3.8 - - + -
153A ASP* 3.5 29.5 + - + +
154A SER* 3.1 23.3 + - - +
156A GLU* 1.3 79.4 - - + +
158A MET* 1.3 59.9 + - - +
160A GLN* 2.6 36.6 + - - +
161A PHE* 3.0 23.6 + - - +
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Residues in contact with MET 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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151A TRP* 3.4 45.6 - - + +
154A SER 2.9 8.0 + - - +
155A ASP* 3.3 26.0 - - - +
157A ARG* 1.3 76.3 - - - +
159A ALA* 1.3 56.0 + - - +
161A PHE* 3.2 4.1 + - - +
162A THR* 3.0 28.4 + - - -
172A PHE* 3.7 20.0 - - + -
179A TRP* 3.6 39.5 - - + +
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Residues in contact with ALA 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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155A ASP 3.0 13.1 + - - +
156A GLU* 3.7 11.7 - - - +
157A ARG 3.3 0.6 - - - -
158A MET* 1.3 75.0 - - - +
160A GLN* 1.3 62.8 + - - +
162A THR* 3.5 10.8 + - - +
163A ALA* 3.3 21.8 + - - +
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Residues in contact with GLN 160 (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 PHE* 3.8 11.0 - - + -
156A GLU* 3.3 27.7 + - - +
157A ARG* 2.6 55.6 + - - +
159A ALA* 1.3 77.9 - - - +
161A PHE* 1.3 55.8 + - - +
163A ALA* 3.9 5.9 - - - +
164A ARG* 3.2 33.5 + - + +
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Residues in contact with PHE 161 (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 LEU* 3.7 23.3 - - + -
107A LEU* 3.8 25.1 - - + -
113A PHE* 3.8 27.3 - + + -
115A PHE* 3.7 28.9 - + - -
149A LEU* 4.4 6.7 - - + -
151A TRP* 3.3 26.5 - + + -
157A ARG 3.0 14.2 + - - +
158A MET 3.3 8.5 - - - +
160A GLN* 1.3 74.5 - - - +
162A THR* 1.3 65.1 + - - +
163A ALA 3.3 0.2 + - - -
164A ARG* 3.3 4.1 + - - +
165A LEU* 3.0 46.9 + - + +
172A PHE* 4.0 27.6 - + - -
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Residues in contact with THR 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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158A MET 3.0 16.8 + - - +
159A ALA* 3.5 11.9 + - - +
161A PHE* 1.3 72.8 - - - +
163A ALA* 1.3 56.1 + - + +
165A LEU* 3.3 5.2 + - - +
166A ASN* 2.8 54.9 + - - +
172A PHE* 3.3 36.2 + - - +
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Residues in contact with ALA 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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159A ALA 3.3 12.9 + - - +
160A GLN* 3.9 7.4 - - - +
161A PHE 3.2 0.4 - - - -
162A THR* 1.3 81.0 - - + +
164A ARG* 1.3 60.7 + - + +
166A ASN* 3.2 8.8 + - - +
167A GLU* 2.9 44.3 + - - +
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Residues in contact with ARG 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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107A LEU* 4.1 28.3 - - + +
111A GLU* 3.6 33.6 + - - +
113A PHE* 4.8 3.6 - - + -
160A GLN* 3.2 22.0 + - + +
161A PHE* 3.7 6.1 - - - +
163A ALA* 1.3 77.3 - - + +
165A LEU* 1.3 61.4 + - - +
167A GLU* 2.9 32.6 + - - +
168A LEU* 3.2 44.5 + - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A VAL* 4.5 2.5 - - + -
104A LEU* 3.9 16.6 - - + -
107A LEU* 3.8 24.7 - - + -
161A PHE* 3.0 44.6 + - + +
162A THR* 3.6 4.5 - - - +
164A ARG* 1.3 74.6 - - - +
166A ASN* 1.3 58.0 + - - +
168A LEU* 2.9 20.8 + - - +
169A GLY 3.2 0.3 + - - -
170A LEU* 2.9 47.8 + - + +
171A GLN 4.5 2.0 - - - +
172A PHE* 3.9 19.7 - - + -
181A VAL* 3.9 23.3 - - + -
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Residues in contact with ASN 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 THR* 2.8 45.5 + - - +
163A ALA* 3.5 7.8 - - - +
165A LEU* 1.3 72.2 - - - +
167A GLU* 1.3 61.8 + - + +
169A GLY* 3.2 12.8 + - - -
170A LEU 3.0 19.0 - - - +
171A GLN* 4.2 8.0 - - - +
172A PHE 4.8 0.2 + - - -
184A ALA* 5.7 0.3 - - - +
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Residues in contact with GLU 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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163A ALA* 2.9 33.7 + - - +
164A ARG* 2.9 38.1 + - - +
166A ASN* 1.3 72.4 - - + +
168A LEU* 1.3 61.7 + - + +
169A GLY 3.3 1.5 + - - -
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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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95A ILE* 5.0 5.0 - - - +
103A VAL* 3.6 36.9 - - + +
107A LEU* 4.7 8.3 - - + -
164A ARG* 3.2 45.0 + - - +
165A LEU* 2.9 10.0 + - - +
167A GLU* 1.3 78.6 - - + +
169A GLY* 1.3 59.1 + - - +
170A LEU* 3.4 11.2 - - + +
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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