Contacts of the helix formed by residues 159 - 172 (chain A) in PDB entry 4B94
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 VAL 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LEU* 4.0 18.8 - - + -
157A GLY* 3.2 15.8 + - - +
158A ASN* 1.3 68.5 - - - +
160A LYS* 1.4 64.9 + - - +
162A SER* 3.4 7.2 + - - -
163A LYS* 3.1 23.7 + - + +
187A LEU* 4.2 21.3 - - + +
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Residues in contact with LYS 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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158A ASN* 3.4 0.6 - - - -
159A VAL* 1.4 78.8 - - - +
161A LYS* 1.4 56.6 + - - +
163A LYS* 3.4 8.1 + - - +
164A GLN* 3.0 58.1 + - + +
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Residues in contact with LYS 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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129A ARG* 5.7 3.8 - - - +
133A GLN* 5.9 3.2 - - - +
136A ARG* 4.7 8.3 - - - +
149A PHE* 4.8 10.3 - - - -
153A GLU* 3.8 24.5 - - + +
158A ASN* 3.5 19.9 + - + +
159A VAL 3.4 0.4 - - - -
160A LYS* 1.4 73.2 - - - +
162A SER* 1.3 59.6 + - - +
164A GLN* 3.3 21.6 + - + +
165A LEU* 2.9 56.1 + - + +
168A LYS* 5.4 5.7 - - - +
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Residues in contact with SER 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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150A ALA* 2.7 40.0 + - - +
153A GLU* 4.0 4.4 - - - +
154A LEU* 3.7 16.9 - - - +
158A ASN 3.0 18.1 + - - -
159A VAL* 3.5 8.1 - - - -
160A LYS 3.3 0.2 - - - -
161A LYS* 1.3 75.6 - - - +
163A LYS* 1.4 58.9 + - - +
165A LEU 3.5 0.5 + - - -
166A LEU* 3.2 25.5 + - - +
187A LEU* 3.8 15.0 - - - +
194A LEU* 4.0 4.2 - - - +
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Residues in contact with LYS 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 VAL* 3.1 14.1 + - + +
160A LYS* 3.7 9.9 - - - +
161A LYS 3.3 0.2 - - - -
162A SER* 1.4 73.7 - - - +
164A GLN* 1.4 59.4 + - + +
166A LEU* 3.3 5.0 + - - +
167A GLN* 2.9 62.0 + - - +
184A LEU* 4.3 9.4 - - + -
187A LEU* 3.5 19.9 - - + +
188A ASN* 4.0 29.2 + - - +
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Residues in contact with GLN 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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160A LYS* 3.0 52.4 + - + +
161A LYS* 3.3 26.2 + - + +
163A LYS* 1.4 74.2 - - + +
165A LEU* 1.3 56.6 + - - +
167A GLN* 3.4 12.4 + - - +
168A LYS* 2.9 33.5 + - - +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ARG* 3.3 38.1 + - - +
146A HIS* 4.5 13.5 + - + +
149A PHE* 3.7 43.1 - - + -
150A ALA* 3.9 17.7 - - + +
153A GLU* 3.7 17.3 - - + -
161A LYS* 2.9 37.8 + - + +
162A SER 3.7 4.0 - - - +
164A GLN* 1.3 76.3 - - - +
166A LEU* 1.3 61.3 + - - +
168A LYS* 3.8 5.8 - - - +
169A ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 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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146A HIS 4.6 1.8 - - - +
147A ILE* 3.8 30.3 - - + +
150A ALA* 3.7 18.2 - - + -
162A SER 3.2 9.6 + - - +
163A LYS 3.7 5.8 - - - +
165A LEU* 1.3 73.6 - - - +
167A GLN* 1.4 64.8 + - - +
169A ALA* 3.4 6.5 + - - +
170A VAL* 3.2 27.9 + - - +
180A LEU* 4.3 9.7 - - + +
183A ALA* 3.9 33.9 - - + +
184A LEU* 3.8 18.4 - - + +
187A LEU* 3.9 26.9 - - + -
194A LEU* 4.2 9.2 - - + -
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Residues in contact with GLN 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 LYS* 2.9 51.0 + - - +
164A GLN* 3.9 12.3 - - - +
166A LEU* 1.4 72.1 - - - +
168A LYS* 1.4 59.6 + - - +
170A VAL* 3.3 9.0 + - - +
171A GLU* 3.0 29.7 + - - +
184A LEU* 4.2 16.2 - - + +
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Residues in contact with LYS 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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136A ARG* 3.4 34.8 - - - +
146A HIS* 5.7 0.7 - - - +
161A LYS* 5.4 5.8 - - - +
164A GLN 2.9 19.9 + - - +
165A LEU* 3.8 6.7 - - - +
166A LEU 3.4 0.4 - - - -
167A GLN* 1.4 77.0 - - - +
169A ALA* 1.4 51.2 + - - +
171A GLU* 3.3 15.0 + - - +
172A ARG* 2.8 84.9 + - - +
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Residues in contact with ALA 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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146A HIS* 3.6 41.0 + - + -
165A LEU 3.1 11.2 + - - +
166A LEU* 3.5 10.3 - - - +
167A GLN 3.3 0.2 - - - -
168A LYS* 1.4 72.8 - - - +
170A VAL* 1.3 62.5 + - - +
172A ARG* 3.5 2.7 + - - -
173A GLY 3.1 4.9 + - - -
174A ALA* 3.0 31.5 + - + -
180A LEU* 3.7 18.8 - - + +
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Residues in contact with VAL 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 LEU 3.2 15.2 + - - +
167A GLN* 3.3 8.9 + - - +
169A ALA* 1.3 75.3 - - - +
171A GLU* 1.3 63.0 + - - +
173A GLY* 3.2 14.3 + - - -
177A LEU* 4.0 23.1 - - + +
180A LEU* 3.8 29.8 - - + -
181A GLU* 5.4 3.8 - - + +
184A LEU* 3.9 18.8 - - + -
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Residues in contact with GLU 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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167A GLN 3.0 16.4 + - - +
168A LYS* 3.5 14.9 - - - +
170A VAL* 1.3 78.6 - - - +
172A ARG* 1.3 78.3 + - - +
173A GLY 3.5 0.9 + - - -
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Residues in contact with ARG 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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136A ARG* 5.0 3.8 - - - +
146A HIS* 6.0 2.9 - - - -
168A LYS* 2.8 63.5 + - - +
169A ALA* 4.3 1.8 - - - +
170A VAL 3.3 0.2 - - - -
171A GLU* 1.3 89.6 + - - +
173A GLY* 1.3 57.7 + - - +
174A ALA 3.6 1.6 - - - -
1201A GOL 3.3 42.5 - - - +
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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