Contacts of the helix formed by residues 168 - 185 (chain D) in PDB entry 3C5C
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 ASP 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39D LYS* 4.1 0.7 - - - -
167D LEU* 1.3 82.8 - - - +
169D PHE* 1.3 61.2 + - - +
170D GLU* 3.6 26.8 - - - +
171D HIS* 2.5 57.8 + - - +
172D VAL* 3.9 6.1 - - - +
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Residues in contact with PHE 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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39D LYS* 3.4 34.4 - - - +
40D PHE* 3.3 32.3 - + - -
43D LYS* 3.7 46.7 - - + +
61D GLU* 6.0 0.9 - - - -
167D LEU 3.7 1.2 + - - -
168D ASP* 1.3 73.4 - - - +
170D GLU* 1.3 81.0 + - + +
172D VAL* 3.2 5.2 + - - +
173D GLN* 2.9 71.1 + - + -
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Residues in contact with GLU 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D ASP* 3.3 20.8 - - - +
169D PHE* 1.3 100.7 + - + +
171D HIS* 1.3 57.8 + - - +
173D GLN* 3.5 13.8 + - - +
174D HIS* 2.9 27.0 + - - +
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Residues in contact with HIS 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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136D LEU* 5.9 2.4 - - + +
162D GLU 4.4 4.0 - - - -
163D VAL* 3.7 22.4 - - + -
164D SER* 3.1 42.7 + - - -
167D LEU* 3.9 20.5 - - + +
168D ASP* 2.5 49.3 + - - +
170D GLU* 1.3 75.1 - - - +
172D VAL* 1.3 65.9 + - + +
174D HIS* 3.4 15.2 + - - +
175D VAL* 3.4 19.1 + - - +
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Residues in contact with VAL 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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36D LEU* 3.6 39.7 - - + +
39D LYS* 4.1 14.1 - - + -
40D PHE* 4.1 12.3 - - + +
163D VAL* 5.2 0.9 - - + -
164D SER 3.3 26.7 - - - +
168D ASP 3.9 6.1 - - - +
169D PHE 3.2 7.1 + - - +
171D HIS* 1.3 86.2 - - + +
173D GLN* 1.3 65.5 + - - +
175D VAL* 3.2 16.3 + - + +
176D PHE* 3.2 32.8 - - + -
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Residues in contact with GLN 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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40D PHE* 3.9 14.1 - - + -
61D GLU* 4.9 3.5 - - - +
169D PHE* 2.9 48.9 + - + +
170D GLU* 3.6 18.6 + - - +
172D VAL* 1.3 77.3 - - - +
174D HIS* 1.3 57.1 + - - +
176D PHE* 3.4 2.1 + - - +
177D HIS* 2.9 61.9 + - + +
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Residues in contact with HIS 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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161D PHE* 3.9 30.0 - + - -
170D GLU 2.9 15.2 + - - +
171D HIS* 3.5 13.4 + - - +
172D VAL 3.2 0.8 - - - -
173D GLN* 1.3 77.3 - - - +
175D VAL* 1.3 63.0 + - - +
177D HIS* 3.2 5.8 + - - +
178D GLU* 2.7 46.3 + - - +
181D ARG* 3.7 15.4 + - - -
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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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36D LEU* 6.1 0.9 - - + -
95D LEU* 4.2 2.6 - - + +
130D LEU* 3.3 15.8 - - + +
132D LEU* 4.0 27.8 - - + -
161D PHE* 3.7 31.4 - - + -
163D VAL* 3.7 20.6 - - + -
171D HIS 3.4 11.8 + - - +
172D VAL* 3.2 21.1 + - + +
174D HIS* 1.3 80.4 - - - +
176D PHE* 1.3 67.7 + - + +
178D GLU* 3.3 5.8 + - - -
179D ALA* 3.0 24.8 + - - +
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Residues in contact with PHE 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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23D LEU* 3.8 15.4 - - + +
25D ILE* 4.2 2.9 - - + -
36D LEU* 3.6 39.9 - - + -
37D THR* 4.1 7.0 - - - -
40D PHE* 3.5 51.4 - + + -
70D LEU* 5.1 0.7 - - + -
72D VAL* 4.2 24.9 - - + -
95D LEU* 3.5 29.4 - - + -
132D LEU* 5.7 0.9 - - + -
172D VAL* 3.2 31.6 + - + -
173D GLN 3.8 1.3 - - - +
175D VAL* 1.3 81.9 - - + +
177D HIS* 1.3 62.8 + - - +
179D ALA* 3.3 8.4 + - - +
180D VAL* 3.2 24.8 + - - +
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Residues in contact with HIS 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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40D PHE* 4.0 8.2 - + - -
61D GLU* 3.6 22.9 - - + -
62D THR 3.5 18.4 + - - -
63D VAL* 3.6 31.0 - - + +
64D ASP 5.7 0.2 - - - -
70D LEU* 6.0 0.6 - - - +
173D GLN* 2.9 56.7 + - + +
174D HIS* 3.6 4.3 - - - +
176D PHE* 1.3 75.7 - - - +
178D GLU* 1.3 60.2 + - - +
180D VAL* 3.1 6.8 + - - +
181D ARG* 2.8 53.7 + - - +
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Residues in contact with GLU 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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130D LEU* 3.9 7.0 - - + -
159D LEU* 3.8 26.8 - - + +
161D PHE* 3.9 18.2 - - + -
174D HIS* 2.7 34.5 + - - +
175D VAL* 3.5 8.3 - - - +
177D HIS* 1.3 73.0 - - - +
179D ALA* 1.3 56.5 + - - +
181D ARG* 3.0 38.1 + - - +
182D GLU* 2.9 39.3 + - - +
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Residues in contact with ALA 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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23D LEU* 3.7 22.9 - - + -
93D ALA* 3.4 16.8 - - + +
95D LEU* 3.7 22.4 - - + -
130D LEU* 3.9 14.5 - - + +
175D VAL 3.0 13.5 + - - +
176D PHE 3.6 8.7 - - - +
177D HIS 3.3 0.4 - - - -
178D GLU* 1.3 75.6 - - - +
180D VAL* 1.3 53.3 + - - +
182D GLU* 3.4 4.5 + - - +
183D ALA* 2.8 27.7 + - - +
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Residues in contact with VAL 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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21D VAL* 4.2 16.6 - - + +
23D LEU* 4.5 1.6 - - + -
63D VAL* 3.9 23.6 - - + -
68D VAL* 3.9 28.9 - - + -
70D LEU* 4.0 30.3 - - + -
176D PHE 3.2 15.1 + - - +
177D HIS* 3.1 8.8 + - - +
179D ALA* 1.3 73.3 - - - +
181D ARG* 1.3 54.1 + - - +
183D ALA* 2.9 9.3 + - - +
184D ARG* 2.6 40.0 + - + +
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Residues in contact with ARG 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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63D VAL* 3.9 14.1 - - + +
64D ASP* 3.1 41.9 + - - +
174D HIS* 3.7 15.5 - - - -
177D HIS* 2.8 26.9 + - - +
178D GLU* 3.0 59.0 + - - +
180D VAL* 1.3 76.5 - - - +
182D GLU* 1.3 54.4 + - + +
184D ARG* 3.6 6.0 - - - +
185D ARG* 2.7 39.5 + - + +
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Residues in contact with GLU 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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93D ALA* 5.0 0.4 - - + -
128D PRO* 3.5 37.3 - - + +
130D LEU* 4.1 7.6 - - + -
159D LEU* 3.6 35.8 - - + +
178D GLU* 2.9 25.6 + - - +
179D ALA* 3.4 10.8 - - - +
181D ARG* 1.3 76.5 - - - +
183D ALA* 1.3 62.2 + - - +
184D ARG 3.5 0.2 + - - -
185D ARG* 3.5 23.0 + - - +
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Residues in contact with ALA 183 (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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21D VAL* 3.9 27.4 - - + -
92D HIS* 3.9 31.9 - - + +
93D ALA* 4.2 1.6 - - + -
128D PRO* 4.0 2.2 - - - +
179D ALA 2.8 15.5 + - - +
180D VAL 2.9 8.3 + - - +
182D GLU* 1.3 76.6 - - - +
184D ARG* 1.3 59.6 + - - +
185D ARG 3.8 2.8 + - - +
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Residues in contact with ARG 184 (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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21D VAL* 6.4 1.3 - - + -
180D VAL* 2.6 26.4 + - + +
181D ARG* 3.8 5.6 - - - +
183D ALA* 1.3 70.3 - - - +
185D ARG* 1.3 63.1 + - - +
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Residues in contact with ARG 185 (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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181D ARG 2.7 22.9 + - - +
182D GLU* 3.6 20.2 - - - +
183D ALA 3.4 2.5 - - - +
184D ARG* 1.3 76.3 - - - +
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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