Contacts of the helix formed by residues 165 - 177 (chain C) in PDB entry 5L5E
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 ASN 165 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163C GLY 3.6 0.4 + - - -
164C ARG* 1.3 84.2 + - - +
166C SER* 1.3 62.5 + - - +
167C LYS* 3.2 5.4 - - - +
168C THR* 3.3 18.0 + - - +
169C VAL* 3.2 17.7 + - - +
200C VAL* 3.5 33.7 - - + +
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Residues in contact with SER 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C CYS* 4.8 0.4 - - - -
161C THR* 3.2 16.4 - - - +
162C ILE* 3.7 25.4 - - - -
163C GLY 2.8 22.1 + - - -
164C ARG 3.1 3.1 - - - -
165C ASN* 1.3 75.2 - - - +
167C LYS* 1.3 60.9 + - - +
169C VAL* 3.7 9.6 - - - -
170C ARG* 2.9 41.3 + - - +
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Residues in contact with LYS 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C LYS* 5.5 8.9 - - - +
165C ASN* 3.2 2.7 - - - -
166C SER* 1.3 82.3 + - - +
168C THR* 1.3 60.9 + - - +
170C ARG* 3.9 20.3 - - - +
171C GLU* 3.2 32.4 + - - +
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Residues in contact with THR 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165C ASN* 3.3 21.0 + - - +
166C SER 3.2 0.2 - - - -
167C LYS* 1.3 78.4 - - - +
169C VAL* 1.3 59.8 + - - +
171C GLU* 3.1 10.8 - - + +
172C PHE* 3.1 23.9 + - - +
199C GLU* 4.5 21.7 - - + +
200C VAL* 4.1 15.5 - - + -
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Residues in contact with VAL 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C CYS* 3.8 13.7 - - - -
32C VAL* 4.3 5.8 - - + -
161C THR* 3.6 31.6 - - - +
165C ASN 3.2 17.7 - - - +
166C SER* 3.7 7.0 - - - -
168C THR* 1.3 72.4 - - - +
170C ARG* 1.3 60.1 + - - +
172C PHE* 3.3 8.5 + - - +
173C LEU* 2.9 32.8 + - + +
196C SER* 3.7 40.6 - - - +
197C LEU* 5.1 1.3 - - + +
199C GLU* 5.2 0.9 - - - -
200C VAL* 4.2 8.5 - - + -
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Residues in contact with ARG 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C TRP* 5.2 1.0 - - - -
160C GLN* 3.4 29.4 + - - +
161C THR* 3.1 33.0 + - + +
162C ILE* 5.0 2.2 - - - +
166C SER* 2.9 30.8 + - - +
167C LYS* 3.9 33.2 - - - +
169C VAL* 1.3 72.9 - - - +
171C GLU* 1.3 61.4 + - - +
173C LEU* 3.8 5.2 - - + +
174C GLU* 2.9 58.4 + - + +
48D SER* 4.3 12.1 - - - +
50D LEU* 4.8 5.4 - - + -
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Residues in contact with GLU 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C LYS* 3.2 22.8 + - - +
168C THR* 3.1 14.8 + - + +
170C ARG* 1.3 80.6 - - - +
172C PHE* 1.3 62.5 + - - +
174C GLU* 3.5 15.9 + - - +
175C LYS* 3.3 39.4 + - - +
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Residues in contact with PHE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C THR 3.1 9.1 + - - +
169C VAL* 3.4 11.2 - - - +
170C ARG 3.2 0.2 - - - -
171C GLU* 1.3 79.7 - - - +
173C LEU* 1.3 62.0 + - + +
175C LYS* 3.2 10.2 - - + +
176C ASN* 2.9 56.1 + - - +
192C LEU* 3.9 20.2 - - + -
195C ARG* 3.5 45.5 - - + -
196C SER* 3.6 33.2 - - - -
199C GLU* 3.7 38.6 - - + +
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Residues in contact with LEU 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C VAL* 3.9 14.6 - - + -
34C VAL* 4.0 23.1 - - + -
159C ALA* 4.4 7.6 - - + -
160C GLN* 4.4 23.3 - - - +
161C THR* 4.4 0.2 - - + -
169C VAL* 2.9 39.2 + - + +
170C ARG* 3.3 6.7 + - - +
172C PHE* 1.3 80.7 - - + +
174C GLU* 1.3 58.0 + - - +
176C ASN* 4.4 1.3 - - - +
177C TYR* 2.8 38.2 + - + +
192C LEU* 4.7 15.5 - - + -
196C SER* 4.2 15.7 - - - -
50D LEU* 3.7 15.3 - - + -
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C ARG* 2.9 35.4 + - + +
171C GLU* 3.8 17.3 - - - +
172C PHE 3.3 0.4 - - - -
173C LEU* 1.3 76.8 - - - +
175C LYS* 1.3 59.2 + - - +
177C TYR 4.2 8.5 - - - +
48D SER* 2.9 23.8 + - - -
49D PRO* 3.7 27.2 - - + +
50D LEU* 3.8 22.1 - - + +
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Residues in contact with LYS 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C GLU* 3.3 31.6 + - - +
172C PHE* 3.2 18.5 - - + +
174C GLU* 1.3 78.6 - - - +
176C ASN* 1.3 73.0 + - - +
177C TYR 3.7 1.5 - - - +
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Residues in contact with ASN 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C PHE* 2.9 50.2 + - + +
173C LEU* 4.4 1.3 - - - +
175C LYS* 1.3 93.9 - - - +
177C TYR* 1.3 62.0 + - - +
178C ASP* 3.6 3.8 + - - +
192C LEU* 4.0 23.9 - - + +
195C ARG* 2.7 30.4 + - - +
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Residues in contact with TYR 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C VAL* 3.9 14.4 - - + -
35C LYS* 2.7 33.2 + - - +
158C SER* 3.7 31.2 + - - -
159C ALA* 4.1 7.6 - - + -
173C LEU* 2.8 27.1 + - + +
174C GLU 4.2 8.8 - - - +
175C LYS 5.0 1.0 - - - -
176C ASN* 1.3 71.7 - - - +
178C ASP* 1.3 75.9 + - - +
179C ARG* 4.0 11.3 + - + +
182C PRO* 3.4 16.5 - - + +
183C PRO* 3.7 15.3 - - + -
192C LEU* 3.9 22.4 - - + -
50D LEU* 3.9 24.1 - - + +
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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