Contacts of the strand formed by residues 133 - 140 (chain A) in PDB entry 3U31
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 GLY 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115A ASN 3.8 4.2 - - - +
116A VAL* 3.5 16.2 - - - +
130A SER* 2.9 27.2 + - - -
131A LEU 3.4 0.8 + - - -
132A HIS* 1.3 82.7 - - - +
134A ASN* 1.3 64.9 + - - +
177A ASN* 3.2 14.8 - - - -
178A ILE* 4.2 0.4 - - - -
179A ILE* 3.9 4.8 - - - +
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Residues in contact with ASN 134 (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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116A VAL* 3.6 6.9 - - - +
118A GLY* 4.1 19.0 - - - +
121A GLU* 4.0 18.2 + - - -
130A SER* 4.6 9.5 + - - +
133A GLY* 1.3 77.3 - - - +
135A VAL* 1.3 60.8 + - - +
136A PHE* 2.9 46.2 + - - +
137A GLU* 3.4 35.4 + - - +
148A LYS* 4.5 2.7 + - - +
177A ASN* 3.0 17.2 + - - +
178A ILE* 3.8 5.1 - - - +
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A TRP* 5.3 1.9 - - - -
81A ILE* 3.4 49.1 - - + -
116A VAL* 2.9 31.7 + - + +
117A ASP* 4.4 1.8 - - - -
134A ASN* 1.3 70.0 + - - +
136A PHE* 1.3 80.3 + - + +
137A GLU 3.3 6.6 + - - +
149A LEU* 4.0 10.7 - - - +
154A LEU* 3.9 12.6 - - + +
176A PRO* 5.5 2.2 - - - +
178A ILE* 3.9 9.4 - - + +
9B MYK 4.1 24.2 - - + -
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Residues in contact with PHE 136 (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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117A ASP 3.5 22.0 - - - -
118A GLY* 4.5 4.3 - - - -
134A ASN* 2.9 22.7 + - - +
135A VAL* 1.3 82.2 - - + +
137A GLU* 1.3 64.1 + - - +
148A LYS* 3.5 13.4 + - - +
149A LEU* 2.8 38.2 + - - +
150A ASN* 3.8 19.5 - - - -
151A LYS* 3.5 35.4 - - + -
154A LEU* 3.9 18.4 - - + -
9B MYK 4.0 20.2 - - + -
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Residues in contact with GLU 137 (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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78A TRP* 5.1 0.3 - - - -
134A ASN* 3.4 26.6 + - - +
135A VAL 3.3 4.7 - - - +
136A PHE* 1.3 85.1 - - - +
138A ALA* 1.3 63.2 + - - +
139A VAL* 5.8 0.2 - - + -
146A ILE* 4.9 13.2 - - + +
147A VAL 3.5 9.4 - - - +
148A LYS* 3.6 20.5 + - + +
149A LEU* 4.5 3.2 - - - +
176A PRO* 3.7 3.3 - - - +
177A ASN* 2.8 49.7 + - + +
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Residues in contact with ALA 138 (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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78A TRP* 3.8 24.2 - - + -
137A GLU* 1.3 77.0 - - - +
139A VAL* 1.3 70.9 + - - +
146A ILE* 3.6 2.3 - - - +
147A VAL* 3.0 33.7 + - + +
149A LEU* 4.1 10.8 - - + -
160A PHE* 4.7 3.4 - - + -
174A PHE* 4.2 13.9 - - + -
175A LYS 3.3 12.6 - - - +
177A ASN 4.0 1.1 - - - +
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Residues in contact with VAL 139 (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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137A GLU* 5.8 0.4 - - + -
138A ALA* 1.3 83.6 - - - +
140A CYS* 1.3 73.6 + - - +
141A CYS* 3.4 2.8 + - + -
144A ASN* 3.3 31.2 - - - +
145A LYS 3.2 11.7 - - - +
146A ILE* 4.7 12.8 - - + -
174A PHE* 3.4 4.5 - - - -
175A LYS* 2.9 35.1 + - + +
176A PRO 5.9 0.2 - - - -
177A ASN* 4.3 25.8 - - + +
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Residues in contact with CYS 140 (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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139A VAL* 1.3 73.4 - - - +
141A CYS* 1.3 61.2 + - - +
142A THR 3.1 12.8 - - - -
143A CYS* 3.4 10.3 - - - -
144A ASN* 2.8 28.1 + - - +
145A LYS* 2.9 13.1 + - + +
168A CYS* 3.6 20.9 - - + -
170A CYS* 3.7 4.9 - - - -
172A GLY* 3.8 9.9 - - - -
173A ILE 3.4 6.7 - - - -
174A PHE* 3.4 9.2 - - + -
276A ZN 2.4 37.2 - - - -
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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