Contacts of the strand formed by residues 157 - 162 (chain A) in PDB entry 6S6A
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 CYS 157 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A TYR* 3.8 4.5 - - - +
122A ILE* 3.3 27.6 - - + +
124A CYS* 3.8 11.4 - - - -
148A LEU* 3.6 9.2 - - - -
149A ARG* 3.3 43.9 - - - +
152A SER* 3.6 18.2 - - - +
155A LEU 3.9 2.0 + - - -
156A GLU* 1.3 76.9 - - - +
158A ALA* 1.3 58.0 + - - +
159A CYS* 3.8 15.2 + - - -
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Residues in contact with ALA 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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122A ILE 3.2 8.0 + - - +
123A PHE* 3.3 30.6 - - + +
124A CYS 3.0 20.4 + - - +
145A GLU* 5.6 0.2 - - - -
157A CYS* 1.3 71.4 - - - +
159A CYS* 1.3 62.2 + - - +
160A PHE* 3.9 13.8 - - + -
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Residues in contact with CYS 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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124A CYS* 3.1 22.0 - - + +
126A VAL* 5.3 0.4 - - + -
141A PHE* 3.6 26.2 - - + -
145A GLU* 3.9 31.2 + - + +
148A LEU* 4.0 18.6 - - + -
149A ARG* 4.6 1.1 - - - +
157A CYS* 3.8 29.4 + - - -
158A ALA* 1.3 72.4 - - - +
160A PHE* 1.3 77.1 + - - +
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Residues in contact with PHE 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.8 27.6 - + + -
124A CYS 3.1 2.8 + - - -
125A LEU* 3.5 15.6 - - + -
126A VAL 2.7 31.5 + - - -
141A PHE* 3.4 11.5 - - - -
158A ALA* 3.9 16.4 - - + -
159A CYS* 1.3 89.1 - - - +
161A ARG* 1.3 55.7 + - - +
162A THR* 3.9 2.9 - - + -
168A THR 5.6 0.4 - - - +
171A LYS* 4.4 20.0 - - + -
172A ALA* 3.8 37.0 - - + -
175A SER* 3.6 33.2 - - - -
176A ILE* 5.8 0.2 - - + -
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Residues in contact with ARG 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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126A VAL 3.2 6.3 - - - +
129A MET* 3.8 22.5 - - + +
134A GLU* 5.9 0.6 - - - +
137A ARG* 3.8 39.9 - - - +
138A ASP* 3.1 38.6 + - - -
141A PHE* 3.6 39.9 - - + -
160A PHE* 1.3 71.1 - - - +
162A THR* 1.3 60.9 - - - +
166A ASP* 5.3 4.2 + - - -
168A THR* 3.3 36.9 - - + +
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Residues in contact with THR 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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23A MET* 3.8 4.9 - - - +
125A LEU* 3.9 19.2 - - + +
126A VAL 2.9 4.7 + - - -
127A HIS* 2.6 36.8 + - - +
128A LYS 3.1 21.3 + - - -
129A MET* 3.2 12.1 + - - +
160A PHE* 4.3 2.7 - - + -
161A ARG* 1.3 74.0 - - - +
163A SER* 1.3 59.3 + - - +
168A THR* 3.4 16.6 - - - +
169A LEU* 4.1 11.0 - - + -
172A ALA* 3.5 31.9 - - + -
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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