Contacts of the helix formed by residues 152 - 163 (chain A) in PDB entry 3KSS
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 ASP 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A LYS 3.9 2.9 + - - +
151A HIS* 1.3 75.0 - - - +
153A LEU* 1.3 82.8 + - - +
154A ALA* 3.5 22.5 + - - +
155A ASP* 3.1 19.4 + - + +
156A LEU* 2.9 33.5 + - - +
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Residues in contact with LEU 153 (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 HIS 4.0 0.4 + - - -
152A ASP* 1.3 82.9 + - - +
154A ALA* 1.3 61.6 + - - +
156A LEU* 3.2 19.5 + - + +
157A ARG* 3.3 11.3 + - - +
182A GLY* 3.3 35.2 - - - +
183A VAL* 3.7 10.3 - - + +
272A ARG* 4.6 5.4 - - - +
283A GLU* 3.4 42.4 - - + +
284A VAL* 5.1 1.6 - - - -
285A ALA* 4.8 9.9 - - + +
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Residues in contact with ALA 154 (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 ASP* 3.3 16.3 - - - +
153A LEU* 1.3 79.7 - - - +
155A ASP* 1.3 62.9 + - - +
157A ARG* 3.6 2.8 + - - +
158A SER* 3.1 26.4 + - - -
183A VAL* 3.3 30.2 - - + +
184A VAL 5.2 0.2 - - - -
185A LYS* 4.6 19.3 - - + +
268A GLY 6.1 0.2 - - - +
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Residues in contact with ASP 155 (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 HIS* 3.6 26.8 + - + +
152A ASP* 3.1 30.5 + - + +
154A ALA* 1.3 79.0 - - - +
156A LEU* 1.3 58.2 + - - +
158A SER* 3.3 8.6 + - - -
159A LEU* 2.8 27.4 + - - +
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Residues in contact with LEU 156 (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 LEU* 3.5 49.1 - - + +
145A VAL* 4.8 0.9 - - - -
146A ASP* 4.5 20.2 - - + +
151A HIS* 4.7 8.5 - - + +
152A ASP 2.9 19.8 + - - +
153A LEU* 3.2 15.0 + - + +
155A ASP* 1.3 73.9 - - - +
157A ARG* 1.3 67.5 + - - +
159A LEU* 2.8 22.1 + - + +
160A GLN* 2.8 15.1 + - - +
284A VAL* 5.0 7.2 - - + -
285A ALA* 4.5 14.1 - - + +
319A VAL* 3.6 22.9 - - + -
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Residues in contact with ARG 157 (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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153A LEU 3.3 4.9 + - - +
154A ALA 3.8 1.8 - - - +
156A LEU* 1.3 76.2 - - - +
158A SER* 1.3 58.2 - - - +
160A GLN* 3.2 6.2 + - - +
161A ASP* 2.7 78.2 + - - +
179A SER* 3.0 26.4 + - - -
180A VAL 5.4 0.9 - - - -
181A GLY 3.1 24.5 + - - +
182A GLY* 3.4 4.2 - - - -
183A VAL 3.3 43.2 - - - +
184A VAL* 5.2 12.0 - - - +
273A ARG* 4.4 4.4 - - - +
285A ALA* 4.1 9.1 - - + +
613A GLU* 2.7 37.8 + - - +
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Residues in contact with SER 158 (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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154A ALA 3.1 12.1 + - - -
155A ASP* 3.4 13.2 - - - -
157A ARG* 1.3 79.7 - - - +
159A LEU* 1.3 61.0 + - - +
162A TRP* 3.1 37.6 + - - +
163A PHE* 5.3 0.2 - - - +
183A VAL 5.3 0.3 + - - -
185A LYS* 4.8 5.2 + - - +
766A TYR* 2.9 38.1 + - - -
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Residues in contact with LEU 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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144A LEU* 4.6 15.7 - - + -
155A ASP* 2.8 15.7 + - - +
156A LEU* 2.8 17.1 + - + +
158A SER* 1.3 77.4 - - - +
160A GLN* 1.3 62.5 + - - +
163A PHE* 3.1 60.4 + - + +
164A LEU* 3.4 7.2 + - + -
315A LEU* 3.9 14.4 - - + -
316A PRO* 3.7 36.3 - - + -
319A VAL* 4.7 3.1 - - + -
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Residues in contact with GLN 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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142A TYR* 2.4 37.3 + - + +
144A LEU* 5.0 7.0 - - + -
156A LEU 2.8 16.0 + - - +
157A ARG* 3.7 10.5 - - - +
159A LEU* 1.3 73.8 - - - +
161A ASP* 1.3 58.2 + - - +
164A LEU* 4.2 12.6 - - + -
165A LYS* 3.1 26.0 + - - +
177A VAL* 3.8 21.6 - - - +
178A ALA 3.9 0.8 + - - -
179A SER* 2.6 31.7 + - - -
285A ALA* 5.6 0.7 - - + -
286A GLY* 3.6 27.5 - - - +
287A GLY* 3.8 6.4 - - - -
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Residues in contact with ASP 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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157A ARG* 2.7 57.5 + - - +
159A LEU 3.2 0.6 - - - -
160A GLN* 1.3 80.4 - - - +
162A TRP* 1.3 93.0 + - + +
163A PHE 3.4 0.2 - - - -
165A LYS* 3.7 15.1 + - - +
166A TYR* 3.6 19.6 - - - -
179A SER* 2.9 15.1 + - - -
184A VAL* 6.0 1.9 - - - +
613A GLU* 5.4 0.7 - - - +
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Residues in contact with TRP 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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158A SER* 3.1 47.2 + - - +
159A LEU 4.2 0.4 - - - -
161A ASP* 1.3 100.3 - - + +
163A PHE* 1.3 61.4 + - - +
166A TYR* 4.3 26.6 + + - -
184A VAL* 5.6 5.6 - - + -
763A ILE* 3.0 43.9 + - + +
764A ALA* 3.6 21.1 - - + +
765A ARG 3.8 19.4 - - - +
766A TYR* 3.1 42.8 - + - -
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Residues in contact with PHE 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 LEU* 3.1 37.2 + - + +
161A ASP 3.4 2.2 + - - -
162A TRP* 1.3 80.5 - - - +
164A LEU* 1.3 100.9 + - + +
165A LYS 3.4 0.4 - - - -
166A TYR* 3.2 8.9 + - - +
167A GLU* 3.0 45.3 + - + +
311A LEU* 4.7 13.2 - - + -
314A SER* 4.3 24.5 - - - -
315A LEU* 5.2 9.9 - - + -
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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