Contacts of the helix formed by residues 158 - 173 (chain C) in PDB entry 4LQL
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 GLU 158 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ALA 3.5 9.3 + - - +
155C ASP* 4.5 9.6 - - - -
156C VAL 3.0 0.8 - - - -
157C GLN* 1.3 78.1 - - - +
159C GLN* 1.3 60.0 + - - +
161C ALA* 3.0 23.4 + - - +
162C ASP* 3.5 8.7 + - - +
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Residues in contact with GLN 159 (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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101C LEU* 5.9 0.5 - - - +
147C VAL* 3.4 32.0 - - + +
155C ASP 3.7 13.7 + - - +
156C VAL* 2.6 19.3 + - - +
158C GLU* 1.3 69.1 - - - +
160C ILE* 1.3 58.6 + - - +
161C ALA 3.0 4.6 + - - -
162C ASP* 3.5 21.1 - - - -
163C TRP* 4.2 5.0 + - - +
461C GLN* 5.3 3.3 + - - +
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Residues in contact with ILE 160 (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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38C LEU* 5.1 15.3 - - + -
44C LEU* 4.3 17.1 - - + +
77C ILE* 5.6 4.3 - - + -
101C LEU* 3.7 29.2 - - + -
103C LEU* 3.9 23.3 - - + -
147C VAL* 4.5 13.5 - - + -
150C TRP 6.3 0.2 - - - -
151C TRP* 5.5 6.5 - - + -
156C VAL* 2.6 35.3 + - + +
157C GLN* 3.8 18.1 + - + +
159C GLN* 1.3 71.2 - - + +
161C ALA* 1.3 65.2 + - - +
163C TRP* 4.5 6.1 - - + +
164C GLN* 3.9 15.2 + - + +
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Residues in contact with ALA 161 (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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43C LYS 5.7 4.5 - - - +
44C LEU* 4.8 2.2 - - + -
45C ASP* 3.0 31.4 - - - -
157C GLN 3.1 15.6 + - - +
158C GLU* 3.0 17.9 + - - +
159C GLN 3.0 0.6 - - - -
160C ILE* 1.3 76.7 - - - +
162C ASP* 1.3 69.5 + - - +
164C GLN* 3.0 13.2 + - - +
165C HIS* 3.6 3.0 + - - -
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Residues in contact with ASP 162 (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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158C GLU 3.5 6.6 + - - +
159C GLN* 3.5 17.5 - - - -
161C ALA* 1.3 77.9 - - - +
163C TRP* 1.3 69.9 + - - +
165C HIS* 2.9 35.1 + - - +
166C VAL* 3.1 9.2 + - - +
458C GLN* 3.6 31.0 - - + -
461C GLN* 4.1 18.2 - - - -
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Residues in contact with TRP 163 (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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9C PHE* 5.1 0.4 - + - -
75C GLY* 3.6 20.0 - - - -
76C VAL 4.0 2.0 - - - -
77C ILE* 4.1 18.4 - - + -
99C PRO* 3.1 45.4 - - + +
100C LEU 3.4 23.6 + - - +
101C LEU* 4.0 35.7 - - + -
144C ALA* 5.5 0.6 - - - +
145C ALA* 4.4 10.4 - - + +
159C GLN 4.2 5.7 + - - +
160C ILE* 4.9 4.5 - - + +
161C ALA 3.2 1.2 + - - -
162C ASP* 1.3 81.1 - - - +
164C GLN* 1.3 66.7 + - + +
166C VAL* 4.1 9.4 - - + -
167C ALA* 2.5 43.1 + - + +
461C GLN* 3.2 33.0 - - + +
465C LEU* 5.1 11.4 - - + +
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Residues in contact with GLN 164 (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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4C MET* 6.5 0.2 - - - -
9C PHE* 4.5 13.2 - - + -
44C LEU* 5.2 4.7 - - + -
45C ASP* 3.3 17.3 - - + -
46C TYR* 3.3 34.8 - - + -
74C ALA* 6.2 1.8 - - + -
75C GLY 6.3 1.1 - - - +
77C ILE* 5.8 0.7 - - + -
160C ILE* 3.9 8.4 + - + +
161C ALA 3.0 11.9 + - - +
162C ASP 2.9 0.2 + - - -
163C TRP* 1.3 90.4 - - + +
165C HIS* 1.3 65.3 + - - +
167C ALA* 3.4 4.3 + - + +
168C VAL* 3.0 29.6 + - + +
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Residues in contact with HIS 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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4C MET* 5.8 9.6 - - + -
45C ASP* 4.6 10.0 - - + +
161C ALA 4.4 6.3 - - - -
162C ASP* 2.9 14.5 + - - +
164C GLN* 1.3 75.8 - - - +
166C VAL* 1.3 55.9 + - + +
168C VAL* 2.9 28.2 + - - +
169C ALA* 3.1 13.0 + - - +
320C ILE 5.5 0.3 - - - +
321C ALA* 4.5 26.8 - - + +
322C ALA* 6.0 1.3 - - - -
323C ASP* 6.0 5.2 - - - -
458C GLN* 6.4 0.7 - - + -
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Residues in contact with VAL 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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162C ASP* 3.1 17.4 + - + +
163C TRP* 3.8 13.9 - - + +
165C HIS* 1.3 72.5 - - + +
167C ALA* 1.3 64.4 + - - +
169C ALA* 3.9 8.7 - - - +
170C TYR* 3.4 20.6 + - - +
321C ALA* 5.2 4.2 - - + +
454C LEU* 5.6 6.1 - - + -
458C GLN* 3.7 32.8 - - + +
461C GLN* 5.1 5.6 - - + +
462C LEU* 4.2 26.4 - - + +
465C LEU* 5.4 5.7 - - + +
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Residues in contact with ALA 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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74C ALA* 4.6 4.8 - - + +
75C GLY 4.4 7.6 - - - +
99C PRO* 3.3 31.8 - - + +
163C TRP* 2.5 58.2 + - + +
164C GLN* 3.4 7.2 - - + +
166C VAL* 1.3 71.7 - - - +
168C VAL* 1.3 68.3 + - - +
170C TYR* 3.8 5.5 + - - +
171C ASN* 4.1 3.5 + - - +
465C LEU* 6.2 0.9 - - - -
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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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3C LYS* 5.6 4.7 - - + -
4C MET* 4.7 22.7 - - + +
7C TYR* 3.9 34.6 - - + -
46C TYR* 5.9 4.5 - - + -
74C ALA* 3.5 27.1 - - + -
164C GLN* 3.0 15.0 + - + +
165C HIS* 2.9 11.7 + - - +
167C ALA* 1.3 77.6 - - - +
169C ALA* 1.3 66.6 + - + +
171C ASN* 3.0 10.7 + - - +
172C GLU* 3.0 24.3 + - + -
320C ILE 5.2 7.9 - - - +
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Residues in contact with ALA 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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165C HIS 3.1 12.2 + - - +
166C VAL* 4.1 8.1 - - - +
167C ALA 3.4 0.4 - - - -
168C VAL* 1.3 77.9 - - - +
170C TYR* 1.3 63.6 + - - +
172C GLU* 3.8 10.8 - - + -
173C SER* 2.9 31.2 + - - +
317C LEU* 4.5 10.1 - - + +
320C ILE* 4.8 6.1 - - + +
321C ALA* 4.3 22.0 - - + -
462C LEU* 5.2 7.2 - - + -
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Residues in contact with TYR 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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99C PRO* 4.7 16.4 - - + -
166C VAL 3.4 12.0 + - - +
167C ALA 4.1 9.0 - - - +
168C VAL 3.3 1.0 + - - -
169C ALA* 1.3 77.2 - - - +
171C ASN* 1.3 63.3 + - - +
173C SER* 3.9 3.7 + - - -
174C PHE* 3.9 11.8 + - - +
462C LEU* 5.3 6.3 - - + +
465C LEU* 4.5 29.8 - - + -
466C PHE* 5.2 10.1 - + + -
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Residues in contact with ASN 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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7C TYR* 4.5 18.8 - - + +
71C ASP 5.8 1.6 - - - +
73C VAL 5.2 1.1 - - - -
74C ALA* 4.8 13.9 - - - -
97C GLN 5.9 1.1 - - - -
98C LYS* 4.9 17.7 - - - -
99C PRO* 4.9 9.4 - - - -
167C ALA 4.1 6.2 + - - +
168C VAL* 3.0 9.5 + - - +
170C TYR* 1.3 78.8 - - - +
172C GLU* 1.3 66.4 + - - +
174C PHE* 3.1 20.6 + - - +
175C HIS* 3.9 9.9 + - - -
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Residues in contact with GLU 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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3C LYS* 5.3 9.9 - - + -
7C TYR* 4.3 22.4 + - + +
168C VAL* 3.0 18.3 + - + +
169C ALA* 2.9 15.3 + - - +
171C ASN* 1.3 76.0 - - - +
173C SER* 1.3 57.4 + - - +
175C HIS* 3.0 34.3 + - - +
176C ILE* 4.3 2.9 - - + +
320C ILE* 3.4 27.4 - - + -
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Residues in contact with SER 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 ALA* 2.9 17.1 + - - +
170C TYR* 4.4 3.8 - - - -
172C GLU* 1.3 74.4 - - - +
174C PHE* 1.3 60.1 + - - +
175C HIS 2.9 5.6 - - - -
176C ILE* 3.1 30.3 + - - +
202C LEU 3.4 14.0 - - - +
203C GLY 3.4 11.8 - - - -
204C TRP* 5.5 0.7 - - - -
317C LEU* 2.9 36.4 - - - +
320C ILE* 5.5 1.0 - - - +
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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