Contacts of the helix formed by residues 154 - 166 (chain A) in PDB entry 5SWW
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 THR 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152A ILE 3.6 13.5 - - - +
153A MET* 1.3 72.3 - - - +
155A TYR* 1.3 67.4 + - - +
156A ASP* 3.2 12.0 + - - +
157A GLU* 2.4 42.0 + - - +
158A PHE* 3.1 21.3 + - - -
179A LEU* 4.5 0.2 - - - -
183A SER* 3.3 19.3 - - - +
187A SER* 4.6 9.2 - - - +
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Residues in contact with TYR 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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154A THR* 1.3 75.4 - - - +
156A ASP* 1.3 70.5 + - - +
158A PHE* 3.9 1.5 - - - +
159A LYS* 2.9 63.4 + - + +
173A PHE* 3.7 35.9 + + - -
175A PRO* 4.2 18.6 - - + +
179A LEU* 3.7 26.1 - - + +
180A ASP* 4.1 16.8 - - - +
183A SER* 4.8 0.6 + - - -
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Residues in contact with ASP 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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154A THR* 3.2 9.8 + - - +
155A TYR* 1.3 92.7 - - - +
157A GLU* 1.3 65.9 + - - +
159A LYS* 3.9 4.8 - - - +
160A HIS* 2.9 29.5 + - - +
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Residues in contact with GLU 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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95A PHE* 3.8 22.2 - - + -
125A PHE* 3.9 33.7 - - + -
152A ILE 4.9 0.9 - - - -
153A MET* 3.7 19.5 - - + -
154A THR* 2.4 52.8 + - - +
156A ASP* 1.3 81.8 - - - +
158A PHE* 1.3 60.6 + - - +
160A HIS* 3.2 6.3 + - - +
161A CYS* 2.9 34.3 + - - -
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Residues in contact with PHE 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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18A PHE* 3.5 13.0 - + + -
22A PHE* 3.2 33.2 - - + -
24A ASN* 3.7 22.9 - - - -
127A ALA* 3.9 11.0 - - + -
153A MET* 3.5 53.6 - - + -
154A THR 3.1 23.4 + - - -
155A TYR 3.9 3.6 - - - +
157A GLU* 1.3 76.4 - - - +
159A LYS* 1.3 57.2 + - - +
161A CYS 3.4 0.7 + - - -
162A TRP* 2.9 28.6 + - - +
173A PHE* 3.6 21.8 - - + -
176A TRP* 3.7 15.3 - + - -
179A LEU* 3.8 18.2 - - + -
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Residues in contact with LYS 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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155A TYR* 2.9 47.7 + - + +
156A ASP* 4.0 4.7 - - - +
158A PHE* 1.3 74.0 - - - +
160A HIS* 1.3 60.2 + - - +
162A TRP* 3.3 1.0 + - - +
163A ASP* 2.9 62.8 + - - +
173A PHE* 3.9 31.8 - - + +
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Residues in contact with HIS 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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36A GLU* 2.6 35.0 + - - -
52A ARG* 6.3 0.4 - - - -
95A PHE* 3.8 21.8 - + + -
156A ASP 2.9 19.6 + - - +
157A GLU* 3.2 7.6 + - - +
159A LYS* 1.3 76.1 - - - +
161A CYS* 1.3 63.3 + - - +
163A ASP* 3.0 8.7 + - - +
164A THR* 2.9 45.9 + - + +
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Residues in contact with CYS 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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18A PHE* 3.6 22.7 - - + -
22A PHE* 5.2 0.7 - - - -
34A CYS* 4.4 7.0 - - - -
95A PHE* 3.4 48.0 - - - -
153A MET* 4.0 5.8 - - - -
157A GLU 2.9 20.5 + - - +
158A PHE* 3.9 0.9 - - - +
160A HIS* 1.3 75.9 - - - +
162A TRP* 1.3 56.6 + - - +
165A PHE* 2.9 48.1 + - + +
166A VAL* 3.3 7.5 + - - +
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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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15A PRO* 3.7 23.8 - - + -
18A PHE* 3.5 24.4 - + + -
19A THR* 3.8 24.0 - - + -
158A PHE 2.9 17.7 + - - +
159A LYS 3.5 4.0 - - - +
160A HIS 3.2 0.2 - - - -
161A CYS* 1.3 78.1 - - - +
163A ASP* 1.3 71.9 + - - +
166A VAL* 3.4 34.6 - - + +
168A HIS* 3.3 33.8 + + + +
171A CYS* 2.8 36.2 + - + -
172A PRO 4.0 7.6 - - - -
173A PHE* 3.3 43.4 - + + +
174A GLN 5.3 2.2 - - - -
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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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159A LYS* 2.9 53.0 + - - +
160A HIS* 3.7 6.8 - - - +
162A TRP* 1.3 94.8 - - - +
164A THR* 1.3 58.5 + - - +
166A VAL 4.7 0.2 - - - +
168A HIS* 3.2 26.7 + - + -
172A PRO* 5.6 1.7 - - - +
173A PHE* 4.9 2.1 + - - +
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Residues in contact with THR 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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12A LEU* 3.8 14.3 - - - +
36A GLU* 4.7 0.9 - - - +
52A ARG* 2.9 43.8 + - - -
160A HIS* 2.9 43.1 + - + +
163A ASP* 1.3 80.6 - - - +
165A PHE* 1.3 91.9 + - + +
166A VAL 3.7 1.1 - - - -
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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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12A LEU* 3.8 10.5 - - - -
13A MET* 2.9 28.5 + - + +
34A CYS* 3.6 35.2 - - + -
35A TYR 3.6 5.4 - - - -
36A GLU* 3.5 35.4 - - + -
52A ARG* 4.0 9.2 - - + -
53A GLY* 3.0 44.0 - - - -
54A PHE* 4.4 9.3 - + + -
95A PHE* 4.1 9.2 - + - -
161A CYS* 2.9 21.7 + - - +
164A THR* 1.3 105.6 - - + +
166A VAL* 1.3 62.4 + - + +
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Residues in contact with VAL 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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12A LEU* 4.1 6.2 - - - +
13A MET* 3.5 16.4 - - + +
15A PRO* 3.7 29.8 - - + -
18A PHE* 3.6 34.3 - - + -
161A CYS 3.3 14.5 + - - +
162A TRP* 3.4 31.3 + - + +
163A ASP 4.7 0.5 - - - +
164A THR 5.1 0.7 - - - -
165A PHE* 1.3 82.1 - - + +
167A ASP* 1.3 64.5 + - - +
168A HIS* 2.8 28.8 + - - +
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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