Contacts of the helix formed by residues 159 - 172 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D LEU* 4.0 18.2 - - + -
157D GLY* 3.3 15.9 + - - +
158D ASN* 1.3 68.9 - - - +
160D LYS* 1.3 64.8 + - - +
162D SER* 3.4 7.9 + - - -
163D LYS* 3.1 24.0 + - + +
187D LEU* 4.2 21.2 - - + +
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Residues in contact with LYS 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D ASN 3.4 0.4 - - - -
159D VAL* 1.3 77.9 - - - +
161D LYS* 1.3 55.6 + - - +
163D LYS* 3.4 6.8 + - - +
164D GLN* 3.0 54.5 + - + +
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Residues in contact with LYS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D ARG* 4.8 15.9 - - - +
136D ARG* 4.9 6.3 - - - +
149D PHE* 4.7 10.3 - - - -
153D GLU* 3.7 24.0 - - + +
158D ASN* 3.5 20.2 + - + +
159D VAL 3.4 0.4 - - - -
160D LYS* 1.3 74.9 - - - +
162D SER* 1.4 59.7 + - - +
164D GLN* 3.3 20.1 + - + +
165D LEU* 2.9 59.5 + - + +
168D LYS* 5.4 5.7 - - - +
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Residues in contact with SER 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D ALA* 2.7 40.0 + - - +
153D GLU* 4.0 4.6 - - - +
154D LEU* 3.7 16.5 - - - +
158D ASN 3.0 18.1 + - - -
159D VAL* 3.5 8.7 - - - -
160D LYS 3.3 0.2 - - - -
161D LYS* 1.4 76.5 - - - +
163D LYS* 1.4 61.0 + - - +
165D LEU 3.5 0.2 + - - -
166D LEU* 3.2 25.8 + - - +
187D LEU* 3.8 15.2 - - - +
194D LEU* 4.1 4.2 - - - +
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Residues in contact with LYS 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D VAL* 3.1 14.1 + - + +
160D LYS* 3.7 9.0 - - - +
162D SER* 1.4 72.9 - - - +
164D GLN* 1.4 59.1 + - + +
166D LEU* 3.3 4.9 + - - +
167D GLN* 2.9 64.6 + - + +
184D LEU* 4.4 11.7 - - + -
187D LEU* 3.5 21.2 - - + +
188D ASN* 4.4 16.0 + - - -
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Residues in contact with GLN 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D LYS* 3.0 44.7 + - + +
161D LYS* 3.7 25.0 + - + +
163D LYS* 1.4 73.3 - - + +
165D LEU* 1.4 56.6 + - - +
167D GLN* 3.4 12.7 + - - +
168D LYS* 2.9 33.3 + - - +
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Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ARG* 3.5 37.1 + - - +
146D HIS* 4.5 13.5 + - + +
149D PHE* 3.7 44.0 - - + -
150D ALA* 3.9 17.7 - - + +
153D GLU* 3.8 17.9 - - + -
161D LYS* 2.9 36.6 + - + +
162D SER 3.7 4.5 - - - +
163D LYS 3.3 0.2 - - - -
164D GLN* 1.4 75.1 - - - +
166D LEU* 1.4 58.7 + - - +
168D LYS* 3.5 5.3 + - + +
169D ALA* 3.1 26.7 + - - +
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Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D HIS 4.6 1.1 - - - +
147D ILE* 3.8 30.5 - - + +
150D ALA* 3.7 17.3 - - + -
162D SER 3.2 10.5 + - - +
163D LYS 3.3 6.0 + - - +
165D LEU* 1.4 73.4 - - - +
167D GLN* 1.3 63.9 + - - +
169D ALA* 3.4 6.5 + - - +
170D VAL* 3.2 27.5 + - - +
180D LEU* 4.4 9.3 - - + +
183D ALA* 3.8 33.7 - - + +
184D LEU* 3.8 19.1 - - + +
187D LEU* 3.9 26.9 - - + -
194D LEU* 4.1 10.1 - - + -
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Residues in contact with GLN 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LYS* 2.9 52.6 + - - +
164D GLN* 3.9 11.6 - - - +
166D LEU* 1.3 71.9 - - - +
168D LYS* 1.4 60.5 + - - +
170D VAL* 3.3 9.0 + - - +
171D GLU* 3.0 29.8 + - - +
184D LEU* 4.2 16.7 - - + +
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Residues in contact with LYS 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ARG* 3.6 26.9 - - - +
146D HIS* 5.5 1.1 - - - +
161D LYS* 5.4 5.9 - - - +
164D GLN 2.9 18.8 + - - +
165D LEU* 3.8 5.8 - - + +
166D LEU 3.4 0.2 - - - -
167D GLN* 1.4 75.3 - - - +
169D ALA* 1.4 55.8 + - - +
171D GLU* 3.3 13.6 + - - +
172D ARG* 2.8 85.8 + - + +
1203D GOL 4.3 7.5 + - - -
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Residues in contact with ALA 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146D HIS* 3.6 38.5 + - + -
165D LEU 3.1 11.0 + - - +
166D LEU 3.5 9.4 - - - +
167D GLN 3.3 0.2 - - - -
168D LYS* 1.4 76.6 - - - +
170D VAL* 1.4 59.6 + - - +
172D ARG* 3.5 3.0 + - - +
173D GLY 3.1 4.9 + - - -
174D ALA* 2.9 31.1 + - + -
180D LEU* 3.7 24.1 - - + +
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Residues in contact with VAL 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D LEU 3.2 15.2 + - - +
167D GLN* 3.3 8.7 + - - +
169D ALA* 1.4 73.5 - - - +
171D GLU* 1.3 64.2 + - - +
173D GLY* 3.2 13.2 + - - -
174D ALA 5.7 0.2 - - - -
177D LEU* 4.1 22.9 - - + +
180D LEU* 3.8 29.8 - - + -
181D GLU* 4.6 7.0 - - - +
184D LEU* 3.9 19.3 - - + -
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Residues in contact with GLU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D GLN 3.0 17.5 + - - +
168D LYS* 3.5 14.9 - - - +
170D VAL* 1.3 78.5 - - - +
172D ARG* 1.3 76.8 + - - +
173D GLY 3.6 0.5 + - - -
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Residues in contact with ARG 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136D ARG* 4.8 0.2 - - - +
146D HIS* 6.0 1.6 - - - -
168D LYS* 2.8 56.7 + - - +
169D ALA* 4.3 1.1 - - - +
170D VAL 3.3 0.2 - - - -
171D GLU* 1.3 89.6 + - - +
173D GLY* 1.3 58.6 + - - +
174D ALA 3.6 1.1 - - - -
1201D GOL 3.2 49.2 + - - +
1203D GOL 3.1 44.8 + - - -
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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