Contacts of the helix formed by residues 161 - 172 (chain A) in PDB entry 6UZA
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 VAL 161 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LEU* 4.2 9.4 - - + -
153A LEU* 4.2 17.5 - - + -
158A LEU* 4.2 30.5 - - + +
159A SER 4.3 4.0 - - - +
160A ARG* 1.3 75.5 - - - +
162A GLY* 1.3 62.2 + - - +
163A ASP 3.3 1.6 - - - -
164A ALA* 3.3 2.5 + - - +
165A LEU* 2.9 27.0 + - - +
180A ILE* 4.1 13.4 - - + +
183A HIS* 4.2 33.9 - - + +
186A PHE* 4.3 7.4 - - + -
206A PHE* 4.9 10.8 + - + -
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Residues in contact with GLY 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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161A VAL* 1.3 78.7 - - - +
163A ASP* 1.3 57.2 + - - +
165A LEU* 3.3 6.6 + - - +
166A LEU* 3.0 23.4 + - - +
186A PHE* 4.4 1.6 - - - -
206A PHE* 4.0 25.4 + - - -
207A TYR* 3.4 35.9 - - - -
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Residues in contact with ASP 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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138A GLN* 2.4 36.0 + - - +
160A ARG* 4.2 4.0 - - + -
161A VAL 3.3 1.4 - - - +
162A GLY* 1.3 73.7 - - - +
164A ALA* 1.3 60.1 + - - +
166A LEU* 3.3 8.3 + - - +
167A LEU* 2.9 27.7 + - - +
206A PHE 4.4 0.6 + - - -
207A TYR* 4.2 13.7 - - - +
208A ALA 3.8 17.5 - - - +
209A TYR* 3.4 9.2 - - + +
215A ARG* 3.0 47.0 + - - +
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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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137A LEU* 3.8 25.4 - - + +
138A GLN* 5.0 6.5 - - + +
141A VAL* 3.5 20.0 - - + +
160A ARG 3.6 19.3 + - - +
161A VAL 3.3 6.8 + - - +
162A GLY 3.3 0.2 - - - -
163A ASP* 1.3 80.2 + - - +
165A LEU* 1.3 56.2 + - - +
167A LEU* 3.4 5.5 + - - -
168A ALA* 3.0 31.0 + - - +
180A ILE* 3.9 7.5 - - + +
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Residues in contact with LEU 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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161A VAL 2.9 14.6 + - - +
162A GLY* 3.5 6.5 - - - +
163A ASP 3.2 0.2 - - - -
164A ALA* 1.3 76.2 - - - +
166A LEU* 1.3 56.2 + - - +
168A ALA* 3.4 2.8 + - - +
169A ILE* 2.9 45.9 + - + +
177A VAL* 4.4 11.2 - - + +
180A ILE* 3.8 28.4 - - + +
181A LEU* 3.8 30.5 - - + -
186A PHE* 3.7 27.6 - - + -
192A LEU* 4.4 0.9 - - + -
207A TYR* 4.7 4.9 - - + -
222A PRO* 3.8 28.9 - - + -
238A LEU* 5.9 0.2 - - + -
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Residues in contact with LEU 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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162A GLY 3.0 18.3 + - - +
163A ASP* 3.8 11.0 - - - +
165A LEU* 1.3 75.9 - - - +
167A LEU* 1.3 57.4 + - - +
169A ILE* 3.4 2.2 + - + -
170A SER* 2.9 29.3 + - - -
207A TYR* 3.7 31.9 - - + +
214A THR* 6.4 0.7 - - - -
215A ARG* 6.0 0.9 - - + +
216A PHE* 4.1 29.4 - - + +
220A VAL* 4.4 12.6 - - + +
221A THR 4.3 3.8 - - - +
222A PRO* 4.0 38.4 - - + -
225A LEU* 3.3 21.9 - - + +
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Residues in contact with LEU 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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134A GLN* 5.2 0.9 - - - +
138A GLN* 4.0 15.0 - - + +
141A VAL* 4.2 9.4 - - + -
142A ALA* 3.9 28.3 - - + +
163A ASP* 2.9 18.6 + - - +
164A ALA* 3.8 4.3 - - - +
166A LEU* 1.3 78.3 - - - +
168A ALA* 1.3 57.5 + - - +
170A SER* 3.3 8.1 + - - +
171A LYS* 3.0 52.6 + - + +
215A ARG* 4.1 39.3 - - - +
216A PHE* 4.7 3.1 - - + -
872D ILE* 6.5 0.7 - - + -
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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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141A VAL* 3.8 7.2 - - + +
164A ALA 3.0 18.1 + - - +
165A LEU 3.9 2.0 - - - +
167A LEU* 1.3 74.5 - - - +
169A ILE* 1.3 60.9 + - - +
172A GLY* 3.0 22.2 + - - -
173A TYR* 3.1 21.0 + - + +
176A ILE* 3.8 28.9 - - + -
177A VAL* 3.7 21.8 - - + +
180A ILE* 4.6 2.0 - - + -
234A ILE* 4.6 0.2 - - - +
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Residues in contact with ILE 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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165A LEU* 2.9 33.8 + - + +
166A LEU* 3.8 5.8 - - - +
168A ALA* 1.3 75.3 - - - +
170A SER* 1.3 64.0 + - - +
172A GLY* 3.5 9.9 + - - -
177A VAL* 3.7 20.0 - - + -
222A PRO* 3.7 33.9 - - + +
225A LEU* 3.9 11.9 - - + -
226A ALA* 3.7 35.7 - - + +
229A CYS* 4.5 2.3 - - - -
231A GLU* 4.0 13.9 - - - +
234A ILE* 3.9 13.5 - - + -
238A LEU* 4.0 13.0 - - + -
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Residues in contact with SER 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 LEU 2.9 18.4 + - - -
167A LEU* 3.6 10.6 - - - +
168A ALA 3.3 0.4 - - - -
169A ILE* 1.3 78.6 - - - +
171A LYS* 1.3 61.9 + - - +
172A GLY 3.7 0.2 + - - -
216A PHE* 3.7 27.6 - - - -
225A LEU* 4.3 5.1 - - - +
229A CYS* 4.2 22.3 - - - +
231A GLU* 4.4 3.8 - - - +
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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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141A VAL 4.6 0.4 - - - +
142A ALA* 3.7 29.1 + - - +
167A LEU* 3.0 40.3 + - + +
168A ALA 4.4 0.2 - - - +
170A SER* 1.3 79.8 - - - +
172A GLY* 1.3 60.8 + - - +
173A TYR* 3.7 45.6 + - + +
231A GLU* 4.5 1.7 - - - +
882A GLY 5.6 3.4 + - - -
885A LYS* 4.3 8.9 - - - +
872D ILE* 6.4 0.8 - - - +
875D GLU* 4.3 12.1 + - - -
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Residues in contact with GLY 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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168A ALA 3.0 6.8 + - - -
169A ILE 3.5 2.2 + - - -
170A SER 3.4 3.0 - - - -
171A LYS* 1.3 79.5 - - - +
173A TYR* 1.3 65.2 + - - +
174A VAL* 3.4 12.4 + - - +
231A GLU* 3.6 29.7 - - - +
234A ILE* 4.4 6.1 - - - -
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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