Contacts of the helix formed by residues 170 - 183 (chain A) in PDB entry 4KLZ
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 TYR 170 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A LYS* 5.9 5.6 - - - -
161A PHE* 4.6 12.5 - + + -
162A GLU 3.4 21.3 - - - +
163A THR* 4.0 4.0 - - + -
168A ARG 3.7 1.8 + - - -
169A TYR* 1.3 127.4 - + - +
171A ILE* 1.3 62.7 + - - +
172A ASP 3.5 2.9 - - - -
173A ASP* 3.6 32.5 + - + +
174A VAL* 3.2 24.9 + - - +
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Residues in contact with ILE 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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37A MET* 3.5 54.7 - - + +
40A GLN* 4.3 5.2 - - + -
41A PHE* 3.7 23.6 - - + +
163A THR* 3.6 24.2 - - + +
165A ALA* 3.9 14.4 - - + -
168A ARG* 4.0 21.2 + - + +
169A TYR 3.2 17.4 - - - +
170A TYR* 1.3 76.6 - - - +
172A ASP* 1.4 62.1 + - - +
174A VAL* 3.4 7.6 + - - +
175A PHE* 3.0 33.6 - - + -
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Residues in contact with ASP 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.4 20.5 - - - +
44A HIS* 5.1 0.9 + - - -
168A ARG* 2.8 40.4 + - - +
170A TYR 3.5 0.2 - - - -
171A ILE* 1.4 73.2 - - - +
173A ASP* 1.3 72.0 + - - +
174A VAL 3.0 1.2 + - - -
175A PHE* 3.1 2.1 + - - -
176A HIS* 3.0 43.5 + - + -
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Residues in contact with ASP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 3.6 22.6 - - + -
170A TYR* 3.6 32.2 + - + +
171A ILE 3.4 0.6 - - - -
172A ASP* 1.3 83.5 + - - +
174A VAL* 1.3 61.3 + - - +
176A HIS* 3.9 6.1 - - - +
177A ALA* 3.0 26.0 + - - +
180A ARG* 5.2 0.3 + - - -
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Residues in contact with VAL 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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37A MET* 4.8 2.7 - - + -
97A ILE* 4.0 17.7 - - + -
130A VAL* 3.8 10.2 - - + +
132A VAL* 3.3 24.9 - - + -
161A PHE* 3.8 26.5 - - + -
163A THR* 3.8 20.9 - - + -
170A TYR 3.2 17.3 - - - +
171A ILE* 3.6 7.9 - - - +
172A ASP 3.0 1.2 + - - -
173A ASP* 1.3 76.8 - - - +
175A PHE* 1.3 70.6 + - + +
177A ALA* 3.5 1.9 + - - +
178A LEU* 2.9 27.7 + - - +
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Residues in contact with PHE 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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24A LEU* 4.3 18.1 - - + +
26A MET* 3.6 40.2 - - + -
37A MET* 4.2 8.3 - - + -
38A THR* 4.1 15.9 - - - -
41A PHE* 3.4 47.8 - + + -
64A ILE* 4.9 0.4 - - - -
71A LEU* 5.0 2.4 - - + +
73A ILE* 4.4 17.3 - - + -
97A ILE* 4.0 9.9 - - + -
171A ILE* 3.0 38.1 - - + -
172A ASP 3.1 1.8 + - - -
174A VAL* 1.3 91.6 - - + +
176A HIS* 1.3 58.0 + - - +
178A LEU* 3.3 6.3 + - - +
179A VAL* 3.0 30.7 + - - +
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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
----------------------------------------------------------
41A PHE* 4.0 24.5 - + - -
62A ILE* 5.1 4.4 - - + +
63A ARG 4.4 14.9 + - - -
64A ILE* 3.5 33.1 - - + +
65A ASP 5.7 0.6 + - - -
172A ASP* 3.0 36.3 + - + +
173A ASP* 3.9 5.5 + - - +
175A PHE* 1.3 76.5 - - - +
177A ALA* 1.3 62.9 + - - +
179A VAL* 3.6 2.4 - - - +
180A ARG* 3.1 49.1 + - - +
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Residues in contact with ALA 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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130A VAL* 4.0 7.6 - - + -
159A PRO* 4.7 8.3 - - + -
161A PHE* 3.5 28.5 - - + -
173A ASP 3.0 17.6 + - - +
174A VAL 3.8 1.1 - - - +
176A HIS* 1.3 73.2 - - - +
178A LEU* 1.3 68.2 + - - +
180A ARG* 3.1 24.7 + - - +
181A GLU* 3.1 15.9 + - - +
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Residues in contact with LEU 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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24A LEU* 4.0 14.4 - - + -
95A GLY* 3.7 8.7 - - - -
96A PHE 3.4 26.5 - - - +
97A ILE* 3.0 37.7 - - + -
128A PRO* 3.8 37.2 - - + +
129A VAL 3.8 2.9 - - - +
130A VAL* 3.6 13.9 - - + +
174A VAL 2.9 18.4 + - - +
175A PHE 3.3 7.4 + - - +
177A ALA* 1.3 69.2 - - - +
179A VAL* 1.3 66.2 + - - +
181A GLU* 3.0 13.3 + - - +
182A ILE* 3.0 15.2 + - + +
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Residues in contact with VAL 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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22A TYR* 4.2 12.8 - - + -
24A LEU* 5.3 1.8 - - + +
64A ILE* 3.0 35.0 - - + -
69A ALA* 5.7 0.2 - - + -
71A LEU* 3.6 28.3 - - + -
175A PHE 3.0 12.9 + - - +
176A HIS 3.6 4.0 - - - +
178A LEU* 1.3 75.4 - - - +
180A ARG* 1.3 60.0 + - - +
182A ILE* 3.3 13.3 + - + +
183A ARG* 2.8 66.0 + - + +
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Residues in contact with ARG 180 (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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64A ILE* 4.4 7.9 - - + +
65A ASP* 3.1 41.0 + - - +
173A ASP 5.2 0.2 + - - -
176A HIS* 3.1 39.8 + - - +
177A ALA* 3.1 24.2 + - - +
179A VAL* 1.3 75.0 - - + +
181A GLU* 1.3 57.8 + - - +
183A ARG* 3.5 13.1 + - - +
184A ARG* 3.1 29.9 + - - +
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Residues in contact with GLU 181 (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 PRO* 3.3 29.4 - - + +
129A VAL 3.9 4.2 - - - +
130A VAL* 3.8 8.8 - - - +
158A CYS* 5.9 0.2 - - - -
159A PRO* 3.5 36.7 - - - +
177A ALA 3.1 19.2 + - - +
178A LEU* 3.0 6.8 + - + +
180A ARG* 1.3 76.0 - - - +
182A ILE* 1.3 68.3 + - - +
184A ARG* 3.8 6.6 - - + +
185A LYS* 3.3 44.8 + - + +
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Residues in contact with ILE 182 (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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22A TYR* 3.3 35.2 - - + -
24A LEU* 3.4 33.0 - - + -
94A GLU* 4.1 38.1 - - + +
95A GLY* 4.2 4.7 - - - -
122A ARG* 6.2 0.7 - - - +
128A PRO* 3.7 10.2 - - + +
178A LEU* 3.0 22.2 + - + +
179A VAL* 3.5 9.9 - - - +
181A GLU* 1.3 75.4 - - - +
183A ARG* 1.3 64.3 + - - +
184A ARG 3.1 0.3 + - - -
185A LYS* 3.0 18.7 - - - +
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Residues in contact with ARG 183 (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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22A TYR* 2.7 37.6 + - + +
64A ILE* 2.9 40.0 + - - +
65A ASP* 4.1 7.7 + - - -
67A GLU* 2.8 46.2 + - - +
69A ALA* 4.6 4.2 - - - +
179A VAL* 2.8 35.9 + - - +
180A ARG* 3.5 13.1 + - - +
181A GLU 3.1 1.0 - - - -
182A ILE* 1.3 79.0 - - - +
184A ARG* 1.4 59.9 + - - +
185A LYS 3.9 4.5 - - - +
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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