Contacts of the strand formed by residues 154 - 160 (chain A) in PDB entry 1U2X
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 VAL 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ALA* 3.9 15.5 - - + +
125A ASN* 4.1 13.2 - - - +
128A ALA* 3.7 23.1 - - + -
135A VAL* 3.7 10.1 - - + +
137A ALA* 3.8 24.0 - - + +
150A PHE* 4.0 7.0 - - + -
151A LYS 3.4 16.6 + - - +
153A GLY* 1.3 76.5 + - - +
155A LEU* 1.3 70.9 + - - +
168A PRO* 3.8 4.4 - - - +
169A ILE* 3.0 40.6 + - + +
170A GLN* 4.4 1.4 + - - -
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Residues in contact with LEU 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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134A LYS* 4.3 28.3 - - + -
135A VAL 3.0 18.1 + - - +
136A ILE* 3.2 11.4 - - + -
137A ALA* 2.7 32.6 + - - +
153A GLY* 3.3 18.4 - - - +
154A VAL* 1.3 78.9 - - - +
156A TYR* 1.3 59.0 + - - +
166A PHE* 3.7 34.1 - - + -
167A LYS 3.5 9.9 - - - +
168A PRO* 5.5 0.9 - - + -
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Residues in contact with TYR 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA 3.1 17.7 - - - -
138A TYR* 3.6 13.2 - + - -
139A THR* 2.7 39.9 + - + -
142A LEU* 3.9 16.5 - - + +
155A LEU* 1.3 74.7 - - - +
157A PRO* 1.3 88.6 - - + +
158A VAL* 3.8 7.0 + - + +
166A PHE* 3.3 6.0 - - - -
167A LYS* 2.9 31.8 + - - +
169A ILE* 3.5 37.2 - - + -
172A ALA* 3.7 18.6 - - + -
174A ARG* 2.6 41.4 + - - -
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Residues in contact with PRO 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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31A TYR* 4.6 4.3 - - + +
136A ILE* 3.9 11.2 - - + -
137A ALA 3.5 15.7 - - - +
138A TYR* 3.8 18.8 - - + -
156A TYR* 1.3 105.5 - - + +
158A VAL* 1.3 59.5 + - - +
164A LEU* 4.0 9.9 - - + -
165A GLN 3.5 7.2 - - - +
166A PHE* 3.9 10.7 - - + -
174A ARG* 5.6 0.3 + - - -
226A ILE* 3.6 16.1 - - + +
233A ILE* 3.7 31.0 - - + -
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Residues in contact with VAL 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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156A TYR* 3.9 22.0 - - + +
157A PRO* 1.3 77.3 - - - +
159A VAL* 1.3 60.4 + - - +
160A GLU* 4.3 15.5 - - + +
164A LEU* 3.6 6.1 - - - +
165A GLN* 2.8 42.9 + - + +
167A LYS* 4.0 32.8 - - + -
172A ALA* 4.1 18.4 - - + +
174A ARG* 5.4 4.7 - - - +
225A ASP* 5.8 0.7 - - - -
226A ILE* 3.6 9.2 - - - -
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Residues in contact with VAL 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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158A VAL* 1.3 74.8 - - - +
160A GLU* 1.3 64.7 + - - +
162A GLY* 4.0 13.9 - - - +
163A GLU 3.3 20.9 - - - +
225A ASP* 3.3 45.0 + - + +
226A ILE* 3.6 17.2 - - + +
229A PHE* 3.8 15.3 - - + -
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Residues in contact with GLU 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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158A VAL* 4.4 5.4 - - + -
159A VAL* 1.3 76.6 - - - +
161A ASN* 1.3 75.2 + - + +
163A GLU* 2.7 23.9 + - - +
165A GLN* 3.3 37.7 + - + +
167A LYS* 2.6 39.0 + - - +
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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