Contacts of the helix formed by residues 164 - 179 (chain A) in PDB entry 2YVC
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 THR 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A LYS* 5.0 9.2 - - - +
163A LEU* 1.3 77.3 - - - +
165A LYS* 1.3 66.3 + - - +
166A GLU* 3.3 19.2 + - - +
167A GLN* 2.8 52.5 + - - +
168A TRP* 3.1 15.4 + - - -
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Residues in contact with LYS 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 LEU 4.2 1.6 + - - -
148A ALA* 2.7 36.4 + - - +
150A ASP 5.3 2.9 + - - -
158A LEU* 6.6 0.4 - - + -
164A THR* 1.3 71.7 - - - +
166A GLU* 1.3 70.8 + - - +
168A TRP* 3.6 8.7 + - - +
169A GLU* 3.0 55.4 + - + +
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Residues in contact with GLU 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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164A THR* 3.3 17.1 - - - +
165A LYS* 1.3 89.2 + - - +
167A GLN* 1.3 59.3 + - + +
169A GLU* 3.8 13.2 - - - +
170A GLU* 3.2 23.4 + - - +
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Residues in contact with GLN 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* 3.5 25.7 - - + +
164A THR* 2.8 55.0 + - - +
166A GLU* 1.3 75.8 - - + +
168A TRP* 1.3 66.6 + - - +
169A GLU 3.0 1.6 - - - -
170A GLU* 2.9 26.0 + - - +
171A ARG* 3.0 17.1 + - + +
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Residues in contact with TRP 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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119A PRO* 4.9 8.5 - - + -
123A VAL* 3.6 32.3 - - + -
153A LEU* 3.7 21.8 - - + -
157A VAL* 4.0 21.5 - - + -
158A LEU* 3.6 26.5 + - + +
161A HIS* 3.3 42.7 + + + -
163A LEU* 3.7 38.2 + - + +
164A THR 3.1 21.1 + - - -
165A LYS* 4.0 9.2 - - - +
167A GLN* 1.3 77.9 - - - +
169A GLU* 1.3 57.3 + - + +
171A ARG* 3.3 19.5 - - - +
172A ILE* 3.1 34.5 + - + +
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Residues in contact with GLU 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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145A GLY* 3.5 27.4 + - - -
146A TYR* 5.6 0.6 - - + -
147A LEU* 3.4 38.2 - - + +
148A ALA* 3.2 8.8 - - - +
152A LEU* 5.4 3.6 - - + -
165A LYS* 3.0 49.3 + - + +
166A GLU* 3.8 11.3 - - - +
167A GLN 3.0 0.4 - - - -
168A TRP* 1.3 77.0 - - + +
170A GLU* 1.3 59.3 + - - +
171A ARG 3.1 0.2 - - - -
172A ILE* 3.3 5.8 + - + +
173A GLN* 2.8 31.7 + - - +
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Residues in contact with GLU 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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166A GLU 3.2 12.1 + - - +
167A GLN* 2.9 19.7 + - - +
169A GLU* 1.3 77.6 - - - +
171A ARG* 1.3 59.4 + - + +
173A GLN* 3.3 20.7 + - - +
174A ASN* 2.9 41.1 + - - +
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Residues in contact with ARG 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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119A PRO* 5.9 0.4 - - - +
120A GLU* 2.8 42.2 + - - -
123A VAL* 4.0 22.0 - - + +
163A LEU* 4.3 19.4 - - + +
167A GLN 3.0 18.9 + - - +
168A TRP* 3.3 28.5 - - - +
169A GLU 3.1 0.2 - - - -
170A GLU* 1.3 77.3 - - + +
172A ILE* 1.3 64.7 + - - +
174A ASN* 3.4 9.9 + - - +
175A TRP* 3.2 36.0 + - - +
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Residues in contact with ILE 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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123A VAL* 4.1 19.3 - - + +
126A ALA* 3.8 19.5 - - + -
127A SER* 3.5 32.1 - - - +
130A VAL* 3.9 13.9 - - + -
147A LEU* 4.5 6.1 - - + -
152A LEU* 3.7 30.3 - - + -
153A LEU* 4.2 13.7 - - + -
168A TRP* 3.1 20.1 + - + +
169A GLU* 3.3 6.5 + - + +
171A ARG* 1.3 72.0 - - - +
173A GLN* 1.3 55.2 + - - +
175A TRP* 3.0 4.1 + - - +
176A HIS* 2.5 35.1 + - - +
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Residues in contact with GLN 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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137A TYR* 3.4 39.8 + - + -
142A HIS 4.6 2.8 - - - +
144A PRO* 5.3 9.0 - - - +
146A TYR* 3.7 31.0 - - + +
147A LEU* 4.5 1.2 - - - +
169A GLU 2.8 18.2 + - - +
170A GLU* 3.3 21.6 + - - +
172A ILE* 1.3 77.1 - - - +
174A ASN* 1.3 56.9 + - - +
176A HIS* 3.0 2.8 + - - +
177A GLU* 2.6 48.5 + - - +
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Residues in contact with ASN 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 GLU* 2.9 29.3 + - - +
171A ARG* 3.5 11.9 - - - +
173A GLN* 1.3 83.1 - - - +
175A TRP* 1.3 62.6 + - + +
177A GLU* 3.4 30.2 + - - +
178A GLU* 3.5 23.6 + - - +
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Residues in contact with TRP 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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120A GLU* 5.0 4.4 + - - -
123A VAL* 3.6 26.9 - - + +
124A LEU* 4.2 38.2 - - + +
127A SER* 3.3 22.7 - - - -
128A TYR* 6.0 0.2 - - - -
171A ARG* 3.2 19.7 + - - +
172A ILE* 3.0 6.9 + - - +
174A ASN* 1.3 76.1 - - + +
176A HIS* 1.3 64.5 + - - +
178A GLU* 3.4 36.7 + - + +
179A HIS* 2.9 30.5 + + - -
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Residues in contact with HIS 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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127A SER* 3.7 3.7 - - - -
130A VAL* 3.4 32.5 - - + +
131A GLN* 3.2 23.7 + - + +
134A TYR* 4.7 3.4 - - + -
135A GLY 2.9 25.4 + - - -
136A ASP 4.1 0.4 - - - -
137A TYR* 3.4 36.4 + + - +
142A HIS* 4.5 5.2 - + - -
146A TYR* 3.1 25.8 + + - +
172A ILE 2.5 23.5 + - - +
173A GLN* 3.0 11.6 + - - +
175A TRP* 1.3 69.7 - - - +
177A GLU* 1.3 64.2 + - - +
178A GLU 3.0 3.5 + - - -
179A HIS* 3.2 15.3 + - - -
180A ARG 4.1 1.6 + - - -
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Residues in contact with GLU 177 (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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137A TYR* 3.8 43.1 + - + +
173A GLN* 2.6 32.0 + - - +
174A ASN* 3.4 30.9 + - - +
175A TRP 3.4 0.2 - - - -
176A HIS* 1.3 72.4 - - - +
178A GLU* 1.3 62.9 + - + +
180A ARG* 3.4 40.8 + - - +
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Residues in contact with GLU 178 (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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174A ASN* 3.5 18.2 - - - +
175A TRP* 3.4 36.3 + - + +
176A HIS 3.0 1.2 - - - -
177A GLU* 1.3 78.3 - - + +
179A HIS* 1.3 60.1 - - + +
180A ARG* 3.1 31.2 + - - +
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Residues in contact with HIS 179 (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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124A LEU* 4.3 0.2 - - - +
127A SER* 3.2 42.5 + - - -
128A TYR* 3.2 45.9 + + - -
131A GLN* 3.7 27.8 + - + +
175A TRP* 2.9 40.6 + + - -
176A HIS* 3.2 4.8 + - - +
178A GLU* 1.3 75.8 - - + +
180A ARG* 1.3 63.9 + - - +
181A GLY 2.9 4.5 + - - -
182A MET* 3.0 28.9 + - + +
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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