Contacts of the helix formed by residues 160 - 173 (chain A) in PDB entry 3FRS
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 ILE 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A PRO* 4.7 9.2 - - + -
159A LYS* 1.3 94.9 - - + +
161A LEU* 1.3 64.1 + - + +
163A GLU* 3.1 16.4 + - + +
164A ARG* 2.8 33.8 - - + +
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Residues in contact with LEU 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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60A ILE* 3.7 28.3 - - + -
64A TYR* 3.6 27.8 - - + +
157A PRO* 4.2 3.4 - - + -
158A PRO* 3.2 37.1 + - + +
160A ILE* 1.3 83.4 - - + +
162A VAL* 1.3 57.2 + - - +
163A GLU 3.1 0.2 - - - -
164A ARG* 3.3 31.3 - - - +
165A TYR* 3.0 43.6 + - + -
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Residues in contact with VAL 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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53A ARG* 3.8 28.9 - - + +
56A VAL* 3.7 17.5 - - + -
57A GLU* 4.2 14.4 - - + +
60A ILE* 3.9 22.2 - - + -
157A PRO* 4.0 15.0 - - + +
158A PRO 3.5 13.5 - - - +
159A LYS* 3.2 13.1 + - - +
161A LEU* 1.3 75.7 - - - +
163A GLU* 1.3 61.4 + - - +
165A TYR* 3.6 4.1 - - - +
166A LEU* 3.2 26.2 + - + +
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Residues in contact with GLU 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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53A ARG* 2.7 44.3 + - - +
159A LYS* 3.0 40.0 - - + +
160A ILE* 3.1 24.0 + - + +
161A LEU 3.1 2.2 + - - -
162A VAL* 1.3 81.2 - - - +
164A ARG* 1.3 51.7 + - - +
166A LEU* 3.4 6.9 - - - +
167A ILE* 2.8 22.1 + - - +
177A TYR* 2.5 46.5 + - - +
180A ASP* 3.8 16.6 + - - +
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Residues in contact with ARG 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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160A ILE* 2.8 32.9 - - + +
161A LEU* 3.3 30.3 - - - +
163A GLU* 1.3 59.6 + - - +
165A TYR* 1.3 79.6 + - - +
167A ILE* 3.4 15.9 - - + +
168A GLU* 2.9 65.6 + - + +
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Residues in contact with TYR 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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37A ARG* 3.7 18.3 + - - +
56A VAL* 3.7 19.3 - - + -
59A ILE* 3.7 21.1 - - + -
60A ILE* 3.6 31.6 + - + +
63A ASP* 2.8 39.8 + - - +
64A TYR* 5.9 2.8 - - - -
67A GLU* 5.7 0.3 + - - -
161A LEU* 3.0 48.7 + - + +
162A VAL 3.9 4.5 - - - +
163A GLU 3.6 1.4 - - - +
164A ARG* 1.3 88.5 - - - +
166A LEU* 1.3 57.6 + - - +
168A GLU* 3.7 7.7 - - - +
169A ILE* 3.1 37.7 + - + +
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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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40A ILE* 4.1 8.3 - - + -
44A LEU* 3.5 17.8 - - + +
49A ASP 5.0 1.1 - - - +
52A ALA* 3.7 38.1 - - + +
53A ARG* 3.9 47.3 - - - +
56A VAL* 4.0 13.2 - - + -
162A VAL* 3.2 19.5 + - + +
163A GLU* 3.4 12.3 - - - +
164A ARG 3.1 0.4 - - - -
165A TYR* 1.3 73.9 - - - +
167A ILE* 1.3 60.0 + - - +
169A ILE* 3.5 2.3 + - - +
170A ALA* 2.9 29.5 + - - +
177A TYR* 3.8 12.6 - - + -
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Residues in contact with ILE 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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163A GLU 2.8 16.5 + - - +
164A ARG* 3.4 26.2 - - + +
166A LEU* 1.3 73.9 - - - +
168A GLU* 1.3 65.3 + - + +
170A ALA* 3.6 4.6 - - - +
171A LYS* 3.0 51.5 + - - +
177A TYR* 4.0 24.2 - - + -
190A GOL 3.8 23.6 - - - +
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Residues in contact with GLU 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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37A ARG* 4.0 17.6 + - - +
164A ARG* 2.9 56.7 + - + +
165A TYR* 3.7 9.7 - - - +
167A ILE* 1.3 81.2 - - + +
169A ILE* 1.3 61.5 + - - +
171A LYS* 3.2 8.9 + - + +
172A ASN* 2.8 44.5 + - - +
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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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37A ARG* 3.3 58.1 - - + +
40A ILE* 3.7 26.2 - - + -
41A ALA* 3.9 20.9 - - + +
44A LEU* 4.5 2.5 - - + -
56A VAL* 3.7 19.5 - - + -
59A ILE* 4.3 4.7 - - + -
165A TYR* 3.1 20.7 + - + +
166A LEU* 3.9 3.6 - - - +
168A GLU* 1.3 73.5 - - - +
170A ALA* 1.3 58.2 + - - +
172A ASN* 4.3 6.7 - - - +
173A TYR* 2.9 35.8 + - + +
175A VAL* 4.4 0.2 - - - +
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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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44A LEU* 3.9 9.1 - - + +
166A LEU 2.9 18.8 + - - +
167A ILE 3.6 5.4 - - - +
169A ILE* 1.3 76.6 - - - +
171A LYS* 1.3 56.2 + - - +
174A ASN 3.0 22.9 + - - -
175A VAL* 3.0 37.7 + - + +
176A PRO 4.5 0.2 - - - +
177A TYR* 3.8 23.6 - - + -
190A GOL 3.3 6.5 + - - -
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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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167A ILE* 3.0 49.4 + - + +
168A GLU* 3.6 9.9 - - + +
170A ALA* 1.3 75.3 - - - +
172A ASN* 1.3 66.3 + - - +
174A ASN* 3.4 18.7 - - - +
190A GOL 4.0 28.2 - - - -
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Residues in contact with ASN 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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37A ARG* 5.0 11.9 - - - +
168A GLU* 2.8 35.3 + - - +
169A ILE* 3.8 6.1 - - - +
171A LYS* 1.3 79.0 - - - +
173A TYR* 1.3 74.4 + - + +
174A ASN* 3.3 7.3 + - - -
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Residues in contact with TYR 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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34A GLN* 3.4 37.9 + - - +
37A ARG* 3.9 18.8 - - + -
38A LYS* 3.6 34.4 + - + +
41A ALA* 3.5 27.4 - - + -
169A ILE* 2.9 25.8 + - + +
172A ASN* 1.3 89.1 - - + +
174A ASN* 1.3 71.7 + - - +
175A VAL* 3.2 11.0 + - + +
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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