Contacts of the helix formed by residues 158 - 176 (chain A) in PDB entry 3E7G
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 LYS 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A TYR* 4.4 11.9 + - + +
154A PHE* 3.7 45.3 - - - +
156A GLU 3.4 6.7 - - - +
157A ALA* 1.3 81.8 - - - +
159A ILE* 1.3 59.3 + - - +
160A GLU 3.3 2.9 - - - -
161A GLU* 3.0 37.2 + - + +
162A HIS* 3.0 28.6 + - - +
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ALA* 4.4 18.1 - - + +
158A LYS* 1.3 68.9 - - - +
160A GLU* 1.3 60.1 + - - +
162A HIS* 3.3 12.0 + - + +
163A LEU* 2.9 43.9 + - + +
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Residues in contact with GLU 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A LYS 3.3 0.6 - - - -
159A ILE* 1.3 77.8 - - - +
161A GLU* 1.3 64.3 + - + +
163A LEU* 3.1 9.9 + - - +
164A ALA* 2.8 29.0 + - + +
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Residues in contact with GLU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR* 3.7 17.6 + - + +
158A LYS* 3.0 46.5 + - + +
160A GLU* 1.3 76.8 - - + +
162A HIS* 1.3 66.8 + - - +
164A ALA* 3.5 7.3 - - - +
165A ARG* 2.9 26.9 + - - +
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Residues in contact with HIS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.1 1.8 - - + -
148A ASN* 2.8 40.5 + - + -
151A TYR* 3.6 46.7 - + + +
152A GLY* 5.5 0.7 - - - -
158A LYS 3.0 17.8 + - - +
159A ILE* 3.5 13.7 - - + +
161A GLU* 1.3 77.2 - - - +
163A LEU* 1.3 61.9 + - + +
165A ARG* 3.4 1.6 + - - +
166A VAL* 3.0 31.4 + - + +
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ILE* 2.9 32.6 + - + +
160A GLU* 3.1 12.5 + - - +
162A HIS* 1.3 75.8 - - + +
164A ALA* 1.3 65.9 + - - +
166A VAL* 3.3 13.0 + - + +
167A GLU* 3.2 40.9 + - + +
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A GLU* 2.8 15.2 + - + +
161A GLU* 3.5 11.7 - - - +
163A LEU* 1.3 75.6 - - - +
165A ARG* 1.3 58.8 + - - +
167A GLU* 3.0 15.0 + - - +
168A ALA* 2.8 29.8 + - - +
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Residues in contact with ARG 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 3.7 19.6 - - + +
151A TYR* 3.5 25.6 - - + +
161A GLU 2.9 16.8 + - - +
162A HIS 3.7 0.9 - - - +
164A ALA* 1.3 76.4 - - - +
166A VAL* 1.3 63.1 + - - +
168A ALA* 3.3 16.1 + - - +
169A VAL* 2.9 54.9 + - + +
172A GLU* 4.5 9.9 + - - -
179A TYR* 4.5 2.8 - - - -
180A GLN 2.8 26.5 + - - -
181A LEU* 3.9 0.6 - - - +
182A THR* 3.7 18.2 - - - +
185A GLU* 2.8 38.4 + - - +
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Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ILE* 4.0 31.0 - - + +
147A VAL* 4.1 11.7 - - + -
148A ASN* 4.6 5.2 - - - +
162A HIS* 3.0 39.0 + - + +
163A LEU* 3.3 13.7 + - + +
165A ARG* 1.3 74.5 - - - +
167A GLU* 1.3 57.7 + - + +
169A VAL* 4.1 4.7 - - - +
170A THR* 2.4 38.4 + - - +
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Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 3.2 32.4 + - + +
164A ALA* 3.0 12.1 + - - +
166A VAL* 1.3 75.6 - - + +
168A ALA* 1.3 66.7 + - - +
170A THR* 2.9 5.4 + - - -
171A LYS* 2.9 50.7 + - + +
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A ALA 2.8 18.9 + - - +
165A ARG* 3.6 21.3 - - - +
167A GLU* 1.3 72.9 - - - +
169A VAL* 1.3 57.9 + - - +
171A LYS* 3.4 4.7 + - - +
172A GLU* 2.8 36.5 + - - +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 5.0 1.6 - - + -
143A ALA* 3.9 17.5 - - + -
144A ILE* 5.1 3.4 - - + -
147A VAL* 4.3 15.0 - - + -
165A ARG* 2.9 58.3 + - - +
166A VAL* 4.1 3.6 - - - +
168A ALA* 1.3 72.9 - - - +
170A THR* 1.3 58.7 + - - +
172A GLU* 4.2 6.1 - - - +
173A ILE* 2.9 55.8 + - + +
179A TYR* 4.0 19.3 - - + -
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Residues in contact with THR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A LEU* 3.8 31.8 - - + +
144A ILE* 4.0 13.9 - - + +
166A VAL* 2.4 30.5 + - - +
167A GLU* 2.9 6.3 + - - -
169A VAL* 1.3 78.5 - - - +
171A LYS* 1.3 75.7 + - + +
173A ILE* 3.5 2.9 + - - +
174A GLU* 3.1 26.1 + - + +
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Residues in contact with LYS 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A GLU* 2.9 47.7 + - + +
168A ALA* 3.9 4.5 - - - +
170A THR* 1.3 84.9 - - + +
172A GLU* 1.3 56.3 + - - +
174A GLU* 2.9 19.3 + - - +
175A THR* 2.7 44.9 + - + +
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Residues in contact with GLU 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A ARG* 4.5 14.0 + - - -
168A ALA* 2.8 20.7 + - - +
169A VAL* 3.7 5.3 - - - +
171A LYS* 1.3 76.7 - - - +
173A ILE* 1.3 57.4 + - - +
175A THR* 3.9 6.1 - - - -
176A THR* 2.8 48.3 + - + +
178A THR 3.6 8.7 - - - +
179A TYR* 3.3 13.9 - - + +
180A GLN* 3.1 35.3 + - - +
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Residues in contact with ILE 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A PRO* 3.9 28.1 - - + +
139A LEU* 4.1 18.2 - - + -
140A LEU* 3.3 36.3 - - + +
143A ALA* 3.7 15.7 - - + -
169A VAL* 2.9 41.4 + - + +
170A THR 3.8 4.5 - - - +
172A GLU* 1.3 75.7 - - - +
174A GLU* 1.3 57.4 + - - +
177A GLY* 3.0 23.3 + - - +
178A THR* 3.5 10.3 - - - +
179A TYR* 4.0 19.3 - - + -
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Residues in contact with GLU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A THR* 3.1 17.5 + - + +
171A LYS* 2.9 22.8 + - - +
173A ILE* 1.3 80.4 - - - +
175A THR* 1.3 67.0 + - - +
176A THR 3.4 0.4 + - - -
177A GLY 4.5 1.4 + - - -
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Residues in contact with THR 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A LYS* 2.7 30.0 + - + +
172A GLU* 3.6 5.0 + - - +
174A GLU* 1.3 81.5 - - + +
176A THR* 1.3 72.5 + - - +
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Residues in contact with THR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLU* 2.8 19.8 + - + +
175A THR* 1.3 91.5 - - - +
177A GLY* 1.3 60.7 + - - +
178A THR* 2.7 36.6 + - - +
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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