Contacts of the helix formed by residues 168 - 179 (chain D) in PDB entry 5DSV
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 ALA 168 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35D THR* 3.2 23.7 + - - +
166D GLY 3.5 3.1 - - - -
167D LYS* 1.3 76.9 - - - +
169D ARG* 1.3 63.6 + - - +
170D GLN* 3.7 4.7 - - + +
171D ALA* 3.6 31.9 - - + +
172D ALA* 3.5 7.8 - - - +
200D VAL* 3.7 15.7 - - + +
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Residues in contact with ARG 169 (chain D).
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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27D MET* 5.2 9.7 + - - +
30D VAL* 3.4 33.1 - - - +
31D GLU* 4.0 20.9 + - - +
134D SER* 4.0 10.9 + - - -
150D MET* 5.7 4.0 - - - +
152D ASP* 5.4 6.9 - - - +
163D CYS* 6.0 0.7 - - - -
164D ALA* 3.4 27.5 + - - +
165D ILE* 4.1 12.2 - - - +
166D GLY 2.8 24.4 + - - +
167D LYS 3.9 0.2 + - - -
168D ALA* 1.3 71.7 - - - +
170D GLN* 1.3 70.0 + - + +
172D ALA* 3.9 2.1 - - - +
173D LYS* 3.1 48.5 + - - +
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Residues in contact with GLN 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 ALA* 3.1 4.7 - - + +
169D ARG* 1.3 80.4 - - + +
171D ALA* 1.3 67.7 + - - +
173D LYS* 3.3 22.1 + - - +
174D THR* 3.0 27.9 + - + +
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Residues in contact with ALA 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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168D ALA* 3.6 20.2 - - + +
170D GLN* 1.3 80.0 - - - +
172D ALA* 1.3 60.3 + - - +
174D THR* 2.9 19.7 + - - -
175D GLU* 3.3 16.5 + - + +
199D ILE* 6.3 0.2 - - + -
200D VAL* 3.9 16.4 - - + -
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Residues in contact with ALA 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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35D THR* 4.2 3.8 - - + -
37D ILE* 4.1 13.0 - - + -
164D ALA* 3.8 16.6 - - + -
168D ALA 3.5 19.1 + - - +
169D ARG 3.4 1.0 + - - -
170D GLN 3.3 0.4 - - - -
171D ALA* 1.3 79.7 - - - +
173D LYS* 1.3 59.7 + - - +
175D GLU* 3.5 3.5 + - - +
176D ILE* 3.1 30.5 + - - +
196D ILE* 4.0 10.4 - - + +
200D VAL* 3.7 18.1 - - + +
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Residues in contact with LYS 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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160D TYR* 5.0 11.0 + - + -
163D CYS* 4.1 19.4 - - + -
164D ALA* 3.9 18.8 - - + +
169D ARG* 3.1 41.6 + - - +
170D GLN* 3.9 16.8 - - - +
171D ALA 3.2 0.4 - - - -
172D ALA* 1.3 73.8 - - - +
174D THR* 1.3 66.0 + - - +
175D GLU 3.1 1.6 - - - -
176D ILE* 3.1 4.9 + - - -
177D GLU* 3.0 21.2 + - - +
54E LEU 5.6 1.2 + - - -
55E SER* 4.8 15.6 - - - +
57E LEU* 3.2 35.1 - - + +
58E TYR* 6.3 0.2 - - - -
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Residues in contact with THR 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 GLN* 3.0 21.7 + - + +
171D ALA* 2.9 18.5 + - - -
173D LYS* 1.3 75.5 - - - +
175D GLU* 1.3 59.8 + - - +
177D GLU* 3.3 36.1 - - - +
178D LYS* 3.6 16.1 + - - +
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Residues in contact with GLU 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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171D ALA* 3.3 16.8 + - + +
172D ALA* 3.5 9.0 - - - +
173D LYS 3.1 0.6 - - - -
174D THR* 1.3 75.4 - - - +
176D ILE* 1.3 62.9 - - - +
178D LYS* 3.2 52.5 + - - +
179D LEU* 4.0 5.2 + - - +
196D ILE* 3.7 33.2 - - + +
199D ILE* 3.5 41.5 - - + +
200D VAL* 4.7 0.7 - - + -
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Residues in contact with ILE 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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37D ILE* 4.2 17.9 - - + -
38D GLY 5.0 2.0 - - - +
39D ILE* 3.7 30.7 - - + -
162D GLY* 4.5 7.9 - - - -
163D CYS* 4.0 26.5 - - - +
164D ALA* 4.3 4.3 - - + -
172D ALA 3.1 22.9 + - - +
173D LYS* 3.1 7.9 + - + +
175D GLU* 1.3 73.0 - - - +
177D GLU* 1.3 65.9 + - - +
178D LYS 3.1 2.0 - - - -
179D LEU* 3.0 20.8 + - - +
181D MET* 3.8 9.3 - - + +
196D ILE* 3.9 19.3 - - + -
57E LEU* 3.4 20.2 - - + -
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Residues in contact with GLU 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 LYS* 3.0 15.1 + - - +
174D THR* 3.3 39.2 + - - +
176D ILE* 1.3 76.7 - - - +
178D LYS* 1.3 61.9 + - - +
179D LEU 3.5 6.2 + - - +
180D GLN* 5.2 1.9 + - - -
181D MET* 4.5 5.7 - - - +
55E SER* 4.3 4.8 + - - -
56E LYS* 3.1 40.0 + - + +
57E LEU* 3.5 23.7 - - + +
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Residues in contact with LYS 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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174D THR* 3.6 15.9 + - - +
175D GLU* 3.2 49.3 + - - +
176D ILE 3.1 0.2 - - - -
177D GLU* 1.3 80.5 - - + +
179D LEU* 1.3 66.1 + - + +
180D GLN* 3.8 12.6 + - - +
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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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39D ILE* 4.1 20.0 - - + -
175D GLU 4.0 10.5 - - - +
176D ILE* 3.0 9.5 + - - +
177D GLU 3.5 3.5 - - - +
178D LYS* 1.3 84.9 - - + +
180D GLN* 1.3 65.6 + - - +
181D MET* 3.4 27.8 - - + +
184D MET* 4.6 9.9 - - + -
189D ILE* 5.4 1.8 - - + -
192D GLU* 3.4 51.4 - - + +
196D ILE* 3.7 22.9 - - + -
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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