Contacts of the strand formed by residues 157 - 165 (chain A) in PDB entry 1X3W
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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148A PRO* 2.9 29.7 - - - +
152A GLU 3.3 22.6 - - - +
153A SER* 4.8 3.8 - - - -
155A PHE 3.1 4.4 + - - -
156A ASN* 1.3 78.4 + - - +
158A GLY* 1.3 58.1 + - - +
159A THR 3.5 29.6 - - - -
160A VAL* 4.1 0.2 - - - -
175A PRO* 4.0 13.2 - - - -
176A ARG 3.5 16.4 - - - +
177A TYR* 3.4 14.8 - - + -
178A ASN* 4.6 0.9 - - - -
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Residues in contact with GLY 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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146A GLN 4.1 0.5 - - - +
147A GLY* 4.0 5.5 - - - -
148A PRO* 3.6 19.8 - - - +
156A ASN* 5.4 0.4 + - - -
157A CYS* 1.3 74.3 - - - +
159A THR* 1.3 65.6 + - - +
176A ARG 4.2 2.4 + - - -
178A ASN* 5.1 2.2 + - - -
2E FRU 5.6 2.7 + - - -
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Residues in contact with THR 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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145A SER* 3.9 25.6 - - - -
146A GLN 3.6 6.2 - - - +
157A CYS* 3.5 3.3 - - - -
158A GLY* 1.3 82.2 + - - +
160A VAL* 1.3 64.6 + - - +
161A GLU* 4.5 8.1 - - + +
176A ARG* 2.7 43.2 + - - +
2E FRU 4.7 14.7 + - - -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A SER* 3.2 2.9 - - - -
146A GLN 2.9 32.0 + - - +
147A GLY 3.8 3.1 - - - +
148A PRO* 3.6 18.8 - - + -
152A GLU* 3.0 27.4 - - - +
157A CYS* 4.1 1.8 - - - -
159A THR* 1.3 79.7 - - - +
161A GLU* 1.3 71.1 + - - +
162A ILE* 3.8 3.3 - - + +
173A ARG* 3.7 34.8 - - + +
174A PHE 3.7 2.7 - - - -
175A PRO* 3.5 29.4 - - + -
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Residues in contact with GLU 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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144A GLY 3.7 5.8 - - - +
145A SER* 4.2 10.8 - - - +
159A THR* 4.2 4.1 - - + +
160A VAL* 1.3 75.8 - - - +
162A ILE* 1.3 59.8 + - - +
163A TYR* 3.0 24.0 + - + +
173A ARG* 3.6 1.7 - - - -
174A PHE* 2.7 43.1 + - + +
176A ARG* 3.3 27.7 + - - -
190A ARG* 2.4 39.5 + - - -
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Residues in contact with ILE 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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142A PRO* 3.8 1.7 - - - +
143A LEU* 3.1 46.4 + - + -
144A GLY 2.9 20.1 + - - +
146A GLN* 3.8 36.3 - - + +
160A VAL 3.8 4.0 - - - +
161A GLU* 1.3 76.8 - - - +
163A TYR* 1.3 71.3 + - - +
171A ILE* 3.2 44.6 - - + -
172A THR 3.9 3.1 - - - -
173A ARG* 4.6 10.8 - - - +
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Residues in contact with TYR 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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125A ASN 4.0 3.1 + - - -
126A LYS* 3.5 32.0 - - + +
127A PRO* 3.6 31.4 - - + -
140A MSE 3.4 24.8 - - + +
141A THR 4.0 2.0 - - - -
142A PRO* 4.0 31.0 - - + +
144A GLY 5.4 0.2 - - - -
161A GLU* 3.0 45.3 + - + +
162A ILE* 1.3 88.6 - - - +
164A LYS* 1.3 60.5 + - - +
171A ILE* 3.2 6.4 - - - +
172A THR 2.8 36.0 + - - +
174A PHE* 4.7 1.1 - - + -
190A ARG* 3.6 7.4 + - - -
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Residues in contact with LYS 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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140A MSE 3.2 6.4 - - - -
141A THR* 2.8 38.8 + - - +
143A LEU* 2.8 26.2 - - + +
163A TYR* 1.3 71.4 - - - +
165A CYS* 1.3 68.0 + - - +
166A ASN* 3.5 10.3 + - - +
169A GLY* 3.4 36.5 + - - -
170A ASN 4.4 0.4 - - - +
171A ILE* 3.6 23.8 - - + +
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Residues in contact with CYS 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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129A CYS* 3.2 15.3 - - - -
132A CYS* 3.4 10.8 - - - -
139A ASN* 4.7 4.0 - - - -
140A MSE 3.5 15.9 - - - +
164A LYS* 1.3 72.8 - - - +
166A ASN* 1.3 58.1 + - - +
167A ARG* 3.1 5.6 + - - -
168A CYS* 3.4 9.0 - - - -
169A GLY* 2.6 35.5 + - - -
170A ASN 3.2 23.9 + - - +
999A ZN 2.3 37.5 - - - -
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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