Contacts of the helix formed by residues 160 - 176 (chain A) in PDB entry 3TKL
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 ASN 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LEU* 4.3 14.9 - - + +
152A GLU* 2.9 31.0 + - - +
153A THR* 3.7 5.8 - - + -
158A ALA 3.3 2.0 + - - -
159A THR* 1.3 81.8 - - - +
161A VAL* 1.3 58.7 + - - +
162A GLU 3.5 2.0 - - - -
163A GLN* 3.8 20.7 - - - +
164A SER* 2.9 33.3 + - - -
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Residues in contact with VAL 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 4.0 23.8 - - + +
30A ARG* 3.9 25.1 - - + -
31A PHE* 3.8 28.5 - - + +
153A THR* 4.5 4.5 - - - -
154A SER 3.5 24.9 - - - +
155A ALA* 4.0 0.2 - - - -
158A ALA* 3.2 18.6 + - + +
159A THR 3.1 4.4 - - - +
160A ASN* 1.3 73.7 - - - +
162A GLU* 1.3 65.9 + - - +
164A SER* 3.2 9.1 + - - -
165A PHE* 3.2 29.2 - - + -
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Residues in contact with GLU 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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31A PHE* 3.5 13.5 - - + -
51A ARG* 2.9 42.9 + - - -
53A ILE* 5.5 1.3 - - - -
158A ALA 4.6 2.0 + - - +
161A VAL* 1.3 79.4 - - - +
163A GLN* 1.3 63.5 + - - +
164A SER 3.3 0.3 + - - -
165A PHE* 3.4 2.4 + - - +
166A MET* 3.0 39.5 + - + +
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Residues in contact with GLN 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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151A LEU* 3.7 15.3 - - + -
160A ASN* 3.5 25.0 + - - +
161A VAL 3.2 0.4 - - - -
162A GLU* 1.3 80.4 - - - +
164A SER* 1.3 57.2 + - - +
166A MET* 3.6 16.1 - - - +
167A THR* 2.8 52.9 + - - +
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Residues in contact with SER 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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27A LEU* 6.4 0.9 - - - -
88A ILE* 5.6 1.6 - - - -
120A LEU* 3.5 26.2 - - - +
122A VAL* 3.9 11.6 - - - +
151A LEU* 3.5 16.2 - - - +
153A THR* 3.3 19.7 - - - +
160A ASN 2.9 23.0 + - - -
161A VAL* 3.5 7.0 - - - -
162A GLU 3.2 0.4 - - - -
163A GLN* 1.3 75.9 - - - +
165A PHE* 1.3 64.7 + - - +
167A THR* 3.2 3.1 + - - -
168A MET* 2.9 23.0 + - - +
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Residues in contact with PHE 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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14A LEU* 3.9 20.3 - - + +
16A LEU* 4.4 17.7 - - + -
27A LEU* 4.3 15.0 - - + -
28A LEU* 4.9 1.3 - - - -
31A PHE* 3.5 61.9 - + + -
53A ILE* 4.8 2.2 - - - -
62A LEU* 4.4 5.1 - - + +
64A ILE* 4.1 23.6 - - + -
88A ILE* 3.7 23.3 - - + -
161A VAL* 3.2 30.1 - - + -
162A GLU 3.4 1.4 + - - +
164A SER* 1.3 80.6 - - - +
166A MET* 1.3 53.3 + - - +
168A MET* 3.2 5.4 + - - +
169A ALA* 2.8 36.4 + - - +
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Residues in contact with MET 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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53A ILE* 3.6 35.9 - - + -
54A GLU 4.1 14.6 - - - +
55A LEU* 3.6 28.5 - - + +
162A GLU* 3.0 32.8 + - + +
163A GLN* 3.6 17.5 - - - +
165A PHE* 1.3 73.4 - - + +
167A THR* 1.3 59.8 + - - +
169A ALA* 3.8 1.0 - - - +
170A ALA* 2.9 30.4 + - - +
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Residues in contact with THR 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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120A LEU* 4.3 8.3 - - + -
149A PRO* 4.0 28.9 - - + -
151A LEU* 4.3 13.7 - - + +
163A GLN* 2.8 42.3 + - - +
164A SER 3.2 5.4 + - - -
166A MET* 1.3 70.2 - - - +
168A MET* 1.3 66.2 + - - +
170A ALA* 3.3 6.3 + - - +
171A GLU* 3.0 33.1 + - + +
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Residues in contact with MET 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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14A LEU* 4.0 29.4 - - + -
86A GLY* 3.8 14.1 - - - -
87A ILE 3.1 42.0 - - - +
88A ILE* 3.8 8.3 - - + -
118A ASN* 3.9 15.9 - - - +
119A LYS 3.7 4.9 - - - +
120A LEU* 3.5 35.8 - - + +
164A SER 2.9 12.4 + - - +
165A PHE* 3.6 10.5 - - - +
167A THR* 1.3 76.3 - - - +
169A ALA* 1.3 63.5 + - - +
171A GLU* 3.1 18.3 + - - +
172A ILE* 3.1 17.6 + - + +
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Residues in contact with ALA 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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12A PHE* 3.5 19.9 - - + -
14A LEU* 5.7 0.4 - - - +
53A ILE* 3.8 23.3 - - + -
55A LEU* 3.9 9.4 - - + +
60A ILE* 4.1 9.9 - - + -
62A LEU* 4.5 8.5 - - + +
165A PHE 2.8 21.8 + - - +
166A MET 3.9 2.5 - - - +
168A MET* 1.3 72.7 - - - +
170A ALA* 1.3 57.9 + - - +
172A ILE* 3.4 1.9 + - - -
173A LYS* 2.9 31.0 + - - +
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Residues in contact with ALA 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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55A LEU* 3.5 19.2 - - + +
56A ASP* 5.9 1.1 - - - +
166A MET 2.9 19.5 + - - +
167A THR* 3.6 7.6 - - - +
168A MET 3.2 0.2 - - - -
169A ALA* 1.3 72.9 - - - +
171A GLU* 1.3 68.2 + - - +
173A LYS* 4.0 2.5 - - - +
174A LYS* 3.2 37.7 + - - +
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Residues in contact with GLU 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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118A ASN* 3.6 32.6 + - + +
119A LYS 5.3 1.3 - - - +
120A LEU* 6.4 0.2 - - + -
147A GLY 5.3 1.7 - - - +
149A PRO* 3.6 33.3 - - + +
167A THR* 3.0 22.3 + - + +
168A MET* 3.1 11.0 + - - +
170A ALA* 1.3 79.0 - - - +
172A ILE* 1.3 61.8 + - - +
174A LYS* 3.5 24.0 + - - +
175A ARG* 3.4 15.2 + - - +
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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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12A PHE* 3.8 33.0 - - + -
14A LEU* 3.8 24.7 - - + -
85A HIS* 3.6 39.5 - - + +
86A GLY* 3.8 3.4 - - - +
118A ASN* 3.5 21.5 - - + +
168A MET* 3.1 18.6 + - + +
169A ALA 3.9 4.7 - - - +
171A GLU* 1.3 73.0 - - - +
173A LYS* 1.3 68.6 + - - +
175A ARG* 3.1 23.5 + - - +
176A MET* 3.3 18.5 + - + +
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Residues in contact with LYS 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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10A TYR* 3.9 31.6 + - + +
12A PHE* 4.0 12.7 - - + -
55A LEU* 4.1 9.2 - - + -
56A ASP* 3.3 30.8 + - - +
58A LYS* 3.7 29.3 - - - +
60A ILE* 4.2 16.6 - - + -
169A ALA 2.9 19.0 + - - +
170A ALA* 4.0 5.4 - - - +
171A GLU 3.4 0.2 - - - -
172A ILE* 1.3 77.3 - - - +
174A LYS* 1.3 61.0 + - - +
176A MET* 3.2 22.6 + - - +
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Residues in contact with LYS 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 ALA* 3.2 30.2 + - - +
171A GLU* 3.5 27.7 + - - +
172A ILE 3.2 0.2 - - - -
173A LYS* 1.3 79.9 - - - +
175A ARG* 1.3 61.7 + - + +
176A MET 3.2 7.7 + - - +
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Residues in contact with ARG 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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84A ALA 4.9 0.4 + - - -
85A HIS* 2.9 49.9 + - - +
116A ASN* 3.4 42.7 + - - +
117A VAL* 4.3 3.0 - - - +
118A ASN* 2.5 26.1 + - - +
171A GLU 3.4 8.5 + - - +
172A ILE* 3.1 20.7 + - - +
174A LYS* 1.3 78.0 - - + +
176A MET* 1.3 67.3 + - + +
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Residues in contact with MET 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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10A TYR* 4.0 20.6 - - + -
11A LEU 5.5 0.7 - - - +
12A PHE* 3.7 28.0 - - + -
85A HIS* 3.8 31.4 - - + +
172A ILE* 3.3 16.4 + - + +
173A LYS* 3.2 15.3 + - - +
174A LYS 3.5 9.4 - - - +
175A ARG* 1.3 92.1 - - + +
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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