Contacts of the helix formed by residues 168 - 179 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35L THR* 3.2 24.3 + - - +
166L GLY 3.5 2.5 - - - -
167L LYS* 1.3 75.8 - - - +
169L ARG* 1.3 63.6 + - - +
170L GLN* 3.7 4.7 - - + +
171L ALA* 3.6 31.4 - - + +
172L ALA* 3.5 7.4 - - - +
200L VAL* 3.7 15.9 - - + +
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Residues in contact with ARG 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27L MET* 5.2 9.5 + - - +
30L VAL* 3.4 33.5 - - - +
31L GLU* 4.0 19.8 + - - +
134L SER* 4.0 11.5 + - - -
150L MET* 5.7 4.4 - - - +
152L ASP* 5.4 6.1 - - - +
163L CYS* 6.0 0.9 - - - -
164L ALA* 3.4 27.1 + - - +
165L ILE* 4.1 12.0 - - - +
166L GLY 2.9 24.2 + - - +
167L LYS 3.9 0.4 + - - -
168L ALA* 1.3 70.8 - - - +
170L GLN* 1.3 68.5 + - + +
172L ALA* 3.9 1.9 - - - +
173L LYS* 3.1 49.2 + - - +
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Residues in contact with GLN 170 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L ALA* 3.1 3.9 - - + +
169L ARG* 1.3 81.8 - - + +
171L ALA* 1.3 66.9 + - - +
173L LYS* 3.3 22.0 + - - +
174L THR* 3.0 28.1 + - + +
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Residues in contact with ALA 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L ALA* 3.6 19.8 - - + +
170L GLN* 1.3 79.4 - - - +
172L ALA* 1.3 60.8 + - - +
174L THR* 2.9 20.0 + - - -
175L GLU* 3.3 16.4 + - + +
200L VAL* 3.9 15.9 - - + -
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Residues in contact with ALA 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35L THR* 4.2 3.8 - - + -
37L ILE* 4.1 13.5 - - + -
164L ALA* 3.8 16.4 - - + -
168L ALA 3.5 19.4 + - - +
169L ARG 3.4 1.0 + - - -
170L GLN 3.3 0.6 - - - -
171L ALA* 1.3 79.8 - - - +
173L LYS* 1.3 60.2 + - - +
175L GLU* 3.5 3.5 + - - +
176L ILE* 3.1 28.7 + - - +
196L ILE* 4.0 10.1 - - + +
200L VAL* 3.7 19.2 - - + +
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Residues in contact with LYS 173 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L TYR* 5.0 9.5 + - + -
163L CYS* 4.1 19.6 - - - -
164L ALA* 3.9 18.8 - - + +
169L ARG* 3.1 42.3 + - - +
170L GLN* 3.9 16.3 - - - +
171L ALA 3.2 0.6 - - - -
172L ALA* 1.3 73.6 - - - +
174L THR* 1.3 65.9 + - - +
175L GLU 3.1 1.6 - - - -
176L ILE* 3.0 5.5 + - + -
177L GLU* 3.0 26.8 + - - +
55M SER* 4.9 15.5 - - - +
57M LEU* 3.6 30.2 - - + +
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Residues in contact with THR 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170L GLN* 3.0 21.4 + - - +
171L ALA* 2.9 18.9 + - - -
173L LYS* 1.3 76.4 - - - +
175L GLU* 1.3 60.1 + - - +
177L GLU* 3.3 34.2 + - - +
178L LYS* 3.6 16.7 + - - +
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Residues in contact with GLU 175 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171L ALA* 3.3 17.5 + - + +
172L ALA* 3.5 9.2 - - - +
173L LYS 3.1 0.6 - - - -
174L THR* 1.3 75.5 - - - +
176L ILE* 1.3 62.5 + - - +
178L LYS* 3.2 52.0 + - - +
179L LEU* 4.0 5.0 + - - +
196L ILE* 3.7 33.4 - - + +
199L ILE* 3.5 41.9 - - + +
200L VAL* 4.7 0.7 - - + -
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Residues in contact with ILE 176 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L ILE* 4.2 17.3 - - + -
38L GLY 4.9 2.2 - - - +
39L ILE* 3.7 29.6 - - + -
162L GLY* 4.5 7.2 - - - -
163L CYS* 4.0 27.4 - - - +
164L ALA* 4.3 4.5 - - + -
172L ALA 3.1 21.1 - - - +
173L LYS* 3.0 10.9 + - + +
175L GLU* 1.3 72.1 - - - +
177L GLU* 1.3 65.5 + - - +
178L LYS 3.1 1.3 - - - -
179L LEU* 3.0 20.8 + - - +
181L MET* 3.8 9.5 - - + +
196L ILE* 3.9 19.5 - - + -
57M LEU* 3.7 18.6 - - + -
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Residues in contact with GLU 177 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173L LYS* 3.0 15.4 + - - +
174L THR* 3.3 39.6 + - - +
176L ILE* 1.3 76.8 - - - +
178L LYS* 1.3 60.6 + - - +
179L LEU 3.5 6.1 + - - +
180L GLN* 5.2 1.9 + - - -
181L MET* 4.5 5.3 - - - +
55M SER* 4.6 3.3 + - - -
56M LYS* 3.6 32.5 + - + +
57M LEU* 3.8 25.7 - - + +
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Residues in contact with LYS 178 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174L THR* 3.6 15.2 + - - +
175L GLU* 3.2 48.5 + - - +
177L GLU* 1.3 79.4 - - - +
179L LEU* 1.3 67.8 + - + +
180L GLN* 3.8 12.6 + - - +
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Residues in contact with LEU 179 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39L ILE* 4.1 20.2 - - + -
175L GLU 4.0 9.9 - - - +
176L ILE* 3.0 10.6 + - - +
177L GLU 3.5 2.8 - - - +
178L LYS* 1.3 86.2 - - + +
180L GLN* 1.3 65.2 + - - +
181L MET* 3.4 28.2 - - + +
184L MET* 4.6 9.0 - - + -
189L ILE* 5.4 2.2 - - + -
192L GLU* 3.4 51.4 - - + +
196L ILE* 3.7 23.6 - - + -
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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