Contacts of the helix formed by residues 162 - 171 (chain A) in PDB entry 3UZU
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 SER 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A ARG* 4.0 16.3 + - - +
160A ALA 4.0 7.0 + - - -
161A PHE* 1.3 76.6 - - - +
163A ARG* 1.3 65.2 + - - +
164A LEU* 3.3 18.6 + - - +
165A SER* 2.9 26.5 + - - -
166A VAL* 3.1 16.1 + - - +
222A PHE* 3.6 15.3 - - - -
225A ARG* 5.0 6.7 - - - +
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Residues in contact with ARG 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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128A PHE* 3.9 25.8 - - + -
162A SER* 1.3 73.6 - - - +
164A LEU* 1.3 55.3 + - - +
166A VAL* 3.3 2.8 + - - +
167A MET* 3.0 33.9 + - + +
218A VAL* 4.0 14.6 - - + -
219A THR* 3.8 39.7 + - - +
222A PHE* 3.6 51.5 + - + +
223A SER* 5.2 1.6 - - - +
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Residues in contact with LEU 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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124A SER* 3.7 21.8 - - - +
127A LEU* 4.4 22.7 - - + -
128A PHE* 3.9 33.1 - - + -
148A VAL* 4.6 9.6 - - + -
151A ARG* 4.6 17.7 - - + +
152A MET* 4.2 20.2 - - + -
162A SER* 3.2 9.5 + - - +
163A ARG* 1.3 76.1 - - - +
165A SER* 1.3 67.7 + - - +
168A LEU* 3.0 54.9 + - + +
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A ARG 2.5 30.7 + - - -
152A MET* 4.0 6.5 - - - +
161A PHE* 3.6 24.5 - - - -
162A SER* 2.9 31.1 + - - -
164A LEU* 1.3 79.3 - - - +
166A VAL* 1.3 56.8 + - - +
169A GLN* 3.0 43.1 + - - +
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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
----------------------------------------------------------
161A PHE* 3.5 31.6 - - + -
162A SER 3.1 10.1 + - - +
163A ARG 3.7 5.4 - - - +
165A SER* 1.3 76.9 - - - +
167A MET* 1.3 60.5 + - - +
170A TYR* 3.0 29.4 + - + +
214A LEU* 5.3 2.2 - - + -
218A VAL* 3.8 31.2 - - + -
222A PHE* 3.9 14.4 - - + -
258A VAL* 3.9 19.6 - - + +
261A TYR* 3.8 22.9 - - + -
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Residues in contact with MET 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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128A PHE* 4.0 25.8 - - + -
131A MET* 3.6 27.2 - - + +
163A ARG* 3.0 22.7 + - + +
164A LEU 4.3 0.7 - - - +
166A VAL* 1.3 76.6 - - - +
168A LEU* 1.3 62.6 + - - +
170A TYR* 3.4 14.8 + - + +
171A ARG 3.3 16.1 + - - -
211A PRO* 4.8 4.9 - - + +
214A LEU* 4.3 20.6 - - + -
215A GLY* 4.1 22.4 - - - +
218A VAL* 4.0 35.2 - - + -
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Residues in contact with LEU 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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127A LEU* 4.3 14.4 - - + +
128A PHE* 5.5 0.4 - - + -
131A MET* 4.1 20.9 - - + -
152A MET* 3.9 34.3 - - + +
164A LEU* 3.0 48.2 + - + +
165A SER 4.3 0.4 - - - +
167A MET* 1.3 78.8 - - + +
169A GLN* 1.3 56.6 + - - +
171A ARG 3.1 0.9 + - - -
172A TYR* 2.9 57.7 + - + +
174A MET* 3.7 16.8 - - + -
198A MET* 4.1 7.6 - - + -
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Residues in contact with GLN 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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152A MET 2.9 18.6 + - - -
153A VAL* 3.6 9.8 + - - +
154A ALA 3.0 27.4 + - - +
156A PRO* 5.6 2.4 - - - +
161A PHE* 4.5 4.2 - - - -
165A SER* 3.0 30.9 + - - +
168A LEU* 1.3 71.5 - - - +
170A TYR* 1.3 65.7 + - - +
172A TYR 3.4 13.2 - - - +
174A MET* 3.6 18.8 - - + -
201A HIS* 4.1 6.4 + - - -
258A VAL* 3.5 26.8 - - + +
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Residues in contact with TYR 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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131A MET* 4.8 3.4 - - + -
166A VAL* 3.0 19.4 + - + +
167A MET* 3.5 18.6 - - + +
168A LEU 3.3 0.2 - - - -
169A GLN* 1.3 76.3 - - - +
171A ARG* 1.3 77.4 + - + +
201A HIS* 3.3 18.4 - - - -
206A LEU* 3.5 25.6 - - + +
207A PRO* 3.9 37.6 + - + +
209A VAL* 4.0 11.4 + - + +
211A PRO* 3.5 33.8 - - + +
214A LEU* 3.4 34.3 - - + -
258A VAL* 3.8 15.8 - - + +
262A VAL* 4.7 2.7 - - + -
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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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131A MET* 3.7 29.3 + - + +
134A ALA* 3.6 28.3 + - + +
135A PRO* 4.1 21.0 - - - +
167A MET 3.3 1.7 + - - +
168A LEU 3.1 2.4 + - - -
170A TYR* 1.3 93.1 - - + +
172A TYR* 1.3 82.9 + - + +
200A PRO* 3.6 6.5 - - - +
201A HIS* 2.9 55.9 + - - +
203A PRO* 5.7 3.8 - - - +
206A LEU* 3.9 28.7 - - - +
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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