Contacts of the helix formed by residues 168 - 182 (chain D) in PDB entry 3IRR
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 PRO 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162D SER* 4.3 1.6 - - - +
166D GLY 4.5 2.2 - - - +
167D THR* 1.3 93.8 - - + +
169D LYS* 1.3 67.0 + - - +
170D LYS* 4.3 10.3 - - + +
171D GLU* 2.9 28.3 + - + +
172D ILE* 3.2 8.3 + - - +
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Residues in contact with LYS 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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158D ALA* 3.8 28.3 - - + +
159D HIS* 3.8 28.6 + - + +
162D SER* 3.6 16.9 + - - +
167D THR 3.3 3.0 + - - -
168D PRO* 1.3 72.3 - - - +
170D LYS* 1.3 62.6 + - - +
172D ILE* 3.2 3.9 + - - +
173D ASN* 3.1 35.7 + - - +
8F C 4.1 9.1 + - - +
9F G 3.3 32.2 + - - +
10F C 4.9 3.8 + - - +
11F G 5.1 2.9 - - - -
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Residues in contact with LYS 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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168D PRO* 4.3 8.3 - - + +
169D LYS* 1.3 81.0 - - - +
171D GLU* 1.3 60.2 + - - +
173D ASN* 3.7 4.0 + - - +
174D ARG* 3.4 46.6 + - - +
10F C 4.0 11.5 + - - +
11F G 3.0 31.4 + - - +
4G G 5.4 3.2 - - - +
5G C 4.1 22.6 + - - +
6G G 4.2 21.7 + - - +
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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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139D MET* 4.1 18.4 - - + +
167D THR* 3.3 24.4 - - + +
168D PRO* 2.9 21.9 + - + +
170D LYS* 1.3 76.7 - - - +
172D ILE* 1.3 66.8 + - - +
173D ASN 3.2 0.4 - - - -
174D ARG* 3.1 23.2 + - + +
175D VAL* 3.4 14.4 + - + +
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Residues in contact with ILE 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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139D MET* 4.2 19.5 - - + -
143D ILE* 4.6 5.8 - - + -
158D ALA* 4.1 8.7 - - + +
161D LEU* 4.1 22.0 - - + +
162D SER* 4.2 10.1 - - - -
165D LEU* 4.3 15.9 - - + -
167D THR* 3.8 31.9 - - + +
168D PRO 3.2 11.6 + - - +
169D LYS* 3.2 10.0 + - - +
171D GLU* 1.3 77.1 - - - +
173D ASN* 1.3 57.8 + - - +
175D VAL* 3.2 8.2 + - - +
176D LEU* 2.9 47.3 + - + +
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Residues in contact with ASN 173 (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 ALA* 3.3 26.4 - - - +
169D LYS* 3.1 22.8 + - - +
170D LYS 3.9 1.8 - - - +
171D GLU 3.2 0.2 - - - -
172D ILE* 1.3 75.1 - - - +
174D ARG* 1.3 64.7 + - - +
176D LEU* 3.7 9.1 - - - +
177D TYR* 2.9 46.9 + - + +
195D TRP* 4.8 2.1 + - - -
10F C 3.4 24.6 + - - -
11F G 2.8 41.8 + - - +
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Residues in contact with ARG 174 (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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170D LYS* 3.4 35.3 + - - +
171D GLU* 3.1 14.0 + - + +
173D ASN* 1.3 78.2 - - - +
175D VAL* 1.3 60.7 + - + +
177D TYR* 4.1 1.3 - - - +
178D SER* 3.1 28.4 + - - -
11F G 2.9 42.7 + - - -
12F C 3.7 34.7 + - - +
13F G 2.7 29.7 + - - -
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Residues in contact with VAL 175 (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 GLY 4.6 11.4 - - - +
139D MET* 3.7 22.0 - - + -
140D GLU* 3.5 36.8 - - + +
143D ILE* 3.6 22.2 - - + -
171D GLU* 3.7 18.8 - - + +
172D ILE* 3.2 5.7 + - - +
173D ASN 3.2 0.6 - - - -
174D ARG* 1.3 76.0 - - + +
176D LEU* 1.3 67.3 + - - +
178D SER* 3.3 5.1 + - - -
179D LEU* 2.9 33.2 + - + +
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Residues in contact with LEU 176 (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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143D ILE* 4.0 21.8 - - + -
147D LEU* 5.5 0.7 - - + -
158D ALA* 3.8 14.4 - - + -
161D LEU* 4.0 12.1 - - + -
172D ILE* 2.9 35.7 + - + +
173D ASN* 3.3 21.7 + - - +
175D VAL* 1.3 78.3 - - - +
177D TYR* 1.3 60.4 + - - +
179D LEU* 3.4 4.7 + - - +
180D ALA 3.2 15.4 + - - -
185D LEU* 3.9 24.1 - - + +
195D TRP* 3.7 50.3 - - + +
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Residues in contact with TYR 177 (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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173D ASN* 2.9 36.8 + - + +
174D ARG 4.4 1.8 - - - +
176D LEU* 1.3 74.3 - - - +
178D SER* 1.3 61.9 + - - +
180D ALA* 3.3 11.2 + - + +
181D LYS* 3.0 39.1 + - - +
187D LYS* 3.5 27.7 + - + +
195D TRP* 3.5 29.3 - + - -
10F C 2.6 28.5 + - - -
11F G 3.4 61.4 - + + +
12F C 5.6 0.4 - - - +
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Residues in contact with SER 178 (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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140D GLU* 4.0 9.0 + - - -
174D ARG 3.1 21.3 + - - -
175D VAL* 3.6 7.9 - - - -
176D LEU 3.3 0.2 - - - -
177D TYR* 1.3 74.7 - - - +
179D LEU* 1.3 65.5 + - - +
181D LYS* 2.9 27.9 + - - +
182D LYS* 3.2 27.4 + - - +
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Residues in contact with LEU 179 (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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140D GLU* 3.8 37.7 - - + +
143D ILE* 4.2 15.0 - - + -
144D LEU* 4.4 20.2 - - + -
175D VAL* 2.9 34.2 + - + +
176D LEU 3.7 4.5 - - - +
178D SER* 1.3 75.5 - - - +
180D ALA* 1.3 60.4 + - - +
182D LYS* 3.1 17.7 + - + +
184D LYS* 3.0 36.3 + - + +
185D LEU* 3.5 34.3 - - + -
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Residues in contact with ALA 180 (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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176D LEU 3.2 10.2 + - - +
177D TYR* 3.3 16.8 - - + +
178D SER 3.1 0.4 - - - -
179D LEU* 1.3 78.2 - - - +
181D LYS* 1.3 64.8 + - + +
183D GLY* 3.1 13.0 + - - -
185D LEU* 3.7 21.9 - - - +
186D GLN* 5.7 0.7 - - - -
187D LYS* 5.7 2.0 - - + +
195D TRP* 4.3 13.2 - - + -
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Residues in contact with LYS 181 (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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177D TYR* 3.0 29.0 + - - +
178D SER* 2.9 16.3 + - - +
180D ALA* 1.3 77.1 - - + +
182D LYS* 1.3 61.4 + - + +
183D GLY 3.3 1.6 + - - -
11F G 6.2 1.4 - - - +
12F C 5.2 9.7 + - - -
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Residues in contact with LYS 182 (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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140D GLU* 2.9 33.3 + - - +
178D SER* 3.4 25.0 + - - +
179D LEU* 3.1 16.0 + - + +
180D ALA 3.1 0.8 - - - -
181D LYS* 1.3 79.6 - - + +
183D GLY* 1.3 63.4 + - - +
184D LYS* 3.3 27.0 + - + +
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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