Contacts of the helix formed by residues 164 - 176 (chain C) in PDB entry 5LEZ
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 GLY 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31C THR* 4.4 1.1 - - - +
162C GLY 3.3 0.6 + - - -
163C ARG* 1.3 74.1 - - - +
165C ALA* 1.3 64.2 + - - +
166C LYS* 3.3 4.0 - - - -
167C SER* 3.6 11.9 + - - -
168C VAL* 3.3 28.7 + - - +
198C VAL* 4.4 10.5 - - - +
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Residues in contact with ALA 165 (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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31C THR* 4.9 0.4 - - - -
160C ALA* 3.7 19.2 - - - +
161C ILE* 3.7 25.4 - - - -
162C GLY 3.0 18.9 + - - +
163C ARG 3.3 0.6 + - - -
164C GLY* 1.3 75.5 - - - +
166C LYS* 1.3 57.0 + - - +
168C VAL* 4.0 0.4 - - - +
169C ARG* 2.7 45.7 + - - +
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Residues in contact with LYS 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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164C GLY* 3.3 2.5 - - - -
165C ALA* 1.3 78.5 - - - +
167C SER* 1.3 58.1 + - - +
169C ARG* 3.6 14.4 + - - +
170C GLU* 3.1 26.3 + - - +
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Residues in contact with SER 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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164C GLY* 3.6 14.8 + - - -
166C LYS* 1.3 76.3 - - - +
168C VAL* 1.3 63.1 + - - +
170C GLU* 3.4 8.2 + - - +
171C PHE* 3.0 26.9 + - - +
197C GLU* 4.7 2.5 - - - +
198C VAL* 5.2 5.5 - - - +
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Residues in contact with VAL 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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31C THR* 4.3 4.9 - - + -
33C VAL* 3.8 18.4 - - + -
160C ALA* 3.6 23.1 - - + -
164C GLY 3.3 18.3 + - - +
165C ALA 3.4 1.4 + - - -
167C SER* 1.3 75.9 + - - +
169C ARG* 1.3 61.0 + - - +
171C PHE* 3.3 7.1 + - - +
172C LEU* 3.0 29.2 + - + +
194C ALA* 3.4 34.5 - - + +
195C LEU* 5.3 0.2 - - - -
197C GLU* 4.9 4.3 - - + +
198C VAL* 3.9 23.6 - - + +
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Residues in contact with ARG 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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146C GLN* 4.8 3.2 + - - -
156C TRP* 3.7 16.0 - - - -
159C ASN* 3.1 31.5 + - - +
160C ALA* 3.5 16.3 + - + +
161C ILE* 5.4 1.2 - - - +
165C ALA* 2.7 34.7 + - - +
166C LYS* 3.9 14.2 - - - +
168C VAL* 1.3 69.0 - - - +
170C GLU* 1.3 61.4 + - - +
172C LEU* 3.3 10.3 + - - +
173C GLU* 2.9 44.5 + - - +
55D THR 5.6 1.1 - - - -
56D SER* 4.1 11.4 - - - -
58D LEU* 4.0 15.9 - - + -
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Residues in contact with GLU 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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166C LYS 3.1 18.3 + - - +
167C SER* 3.6 9.4 - - - +
168C VAL 3.3 0.2 - - - -
169C ARG* 1.3 74.8 - - - +
171C PHE* 1.3 61.4 + - - +
173C GLU* 3.5 16.7 + - - +
174C LYS* 3.4 21.1 + - - +
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Residues in contact with PHE 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 SER 3.0 12.6 + - - +
168C VAL* 3.5 7.6 - - - +
170C GLU* 1.3 77.1 - - - +
172C LEU* 1.3 60.6 + - + +
174C LYS* 3.4 2.5 + - - -
175C ASN* 2.8 74.7 + - + +
190C LEU* 4.2 9.0 - - + -
193C LYS* 3.7 24.5 - - + -
194C ALA* 3.6 33.7 - - + -
197C GLU* 3.0 42.0 - - - +
236C LYS* 4.5 11.0 - - - -
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Residues in contact with LEU 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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33C VAL* 4.1 16.4 - - + -
35C VAL* 4.7 3.4 - - + -
158C ALA* 4.4 13.9 - - + -
159C ASN* 3.9 37.9 - - - +
160C ALA 4.3 0.9 - - - +
168C VAL* 3.0 26.8 + - + +
169C ARG* 3.3 6.5 + - - +
171C PHE* 1.3 73.9 - - + +
173C GLU* 1.3 60.9 + - - +
175C ASN* 4.3 1.3 - - - +
176C TYR* 2.8 38.0 + - + +
190C LEU* 4.3 27.4 - - + +
194C ALA* 4.0 20.4 - - + -
58D LEU* 3.8 11.6 - - + +
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Residues in contact with GLU 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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169C ARG* 2.9 28.8 + - - +
170C GLU* 3.6 17.4 - - - +
171C PHE 3.3 0.2 - - - -
172C LEU* 1.3 77.4 - - - +
174C LYS* 1.3 60.9 + - - +
176C TYR 4.5 6.4 + - - +
55D THR 4.5 2.1 - - - +
56D SER* 2.9 29.2 + - - +
57D PRO* 3.6 24.1 - - + +
58D LEU* 3.6 23.4 - - + +
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Residues in contact with LYS 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 GLU 3.4 10.1 + - - +
171C PHE* 4.0 2.9 - - - +
172C LEU 3.3 0.2 - - - -
173C GLU* 1.3 79.1 - - - +
175C ASN* 1.3 71.9 + - - +
176C TYR 3.8 0.2 - - - -
177C THR* 4.7 10.0 - - - +
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Residues in contact with ASN 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 PHE* 2.8 61.5 + - + +
172C LEU 4.4 0.2 - - - +
174C LYS* 1.3 87.0 - - - +
176C TYR* 1.3 60.6 + - - +
177C THR* 3.3 8.4 + - - -
180C ALA* 3.5 17.3 - - - +
190C LEU* 3.9 20.3 - - + +
236C LYS* 5.4 2.6 - - - +
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Residues in contact with TYR 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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35C VAL* 4.0 4.7 - - + -
36C ARG* 2.9 33.0 + - - -
157C LYS* 3.6 51.9 - - + +
158C ALA* 4.0 15.7 - - + -
172C LEU* 2.8 24.7 + - + +
173C GLU 4.7 5.6 - - - +
174C LYS 3.8 0.4 - - - -
175C ASN* 1.3 70.2 - - - +
177C THR* 1.3 67.6 - - - +
181C ILE* 3.5 33.0 - - + +
190C LEU* 4.0 21.7 - - + +
58D LEU* 4.0 14.1 - - + -
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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