Contacts of the strand formed by residues 146 - 153 (chain A) in PDB entry 1XZ6
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 ARG 146 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A ARG* 4.5 9.1 - - - +
113A ASN* 3.7 33.2 + - - -
114A THR 3.6 7.2 + - - +
115A THR* 3.0 35.1 + - + +
116A ILE* 2.9 31.3 + - - +
145A HIS* 1.3 72.8 - - - +
147A VAL* 1.3 60.2 + - - +
167A GLY* 3.3 19.7 + - - +
169A GLN* 5.3 8.9 - - - +
203A GLU 4.9 5.3 + - - -
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Residues in contact with VAL 147 (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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115A THR* 5.0 1.6 - - - -
116A ILE* 3.3 11.2 - - + +
118A LEU* 4.9 0.9 - - + -
141A PHE* 4.2 13.0 - - + +
142A MET* 3.6 25.4 - - + -
145A HIS 3.4 2.5 + - - +
146A ARG* 1.3 81.0 - - - +
148A HIS* 1.3 69.4 + - - +
149A TYR* 4.1 30.5 - - + -
167A GLY 3.3 7.2 + - - +
168A ARG* 3.3 38.5 - - + +
169A GLN* 2.9 26.7 + - - +
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Residues in contact with HIS 148 (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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115A THR* 4.7 5.4 - - + +
116A ILE 2.9 7.3 + - - -
117A GLY* 3.2 3.6 - - - -
118A LEU 3.0 22.7 + - - -
147A VAL* 1.3 75.6 - - - +
149A TYR* 1.3 74.0 + - - +
150A TYR* 3.3 27.0 + + + -
169A GLN* 3.3 42.3 + - + +
171A SER* 2.7 28.5 + - - -
203A GLU* 3.5 34.4 + - + +
204A VAL* 4.0 12.5 - - + +
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Residues in contact with TYR 149 (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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118A LEU* 3.4 31.9 - - + +
133A PHE* 5.0 1.1 - + - -
134A LEU* 3.8 21.3 - - + -
137A ALA* 3.6 29.4 - - + +
138A GLU* 2.6 35.5 + - + +
141A PHE* 4.9 0.4 - + - -
147A VAL* 4.1 13.5 - - + -
148A HIS* 1.3 77.4 - - - +
150A TYR* 1.3 59.9 + - - +
151A VAL* 4.0 3.8 - - + -
164A LEU* 3.9 15.5 - - + -
168A ARG* 2.9 24.0 + - + -
169A GLN 2.8 30.6 + - - +
170A LEU* 3.9 23.1 - - + -
171A SER 2.8 27.5 + - - -
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Residues in contact with TYR 150 (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 GLY* 4.1 5.4 - - - -
118A LEU 2.8 10.7 + - - +
119A THR* 3.4 20.3 - - + -
120A VAL* 3.1 26.7 + - - +
148A HIS* 3.3 46.8 + + + -
149A TYR* 1.3 71.5 - - - +
151A VAL* 1.3 61.6 + - - +
152A PHE* 3.8 12.7 + - + -
171A SER* 3.6 7.6 - - - -
173A LEU* 4.1 15.7 - - + -
199A ARG* 4.1 13.2 - - - -
200A PHE* 3.6 35.6 - + - -
203A GLU* 2.6 45.0 + - - +
204A VAL* 3.7 12.1 - - + +
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Residues in contact with VAL 151 (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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120A VAL* 3.6 18.8 - - + -
122A ALA* 4.7 2.2 - - + -
130A LEU* 3.9 37.0 - - + -
134A LEU* 4.8 5.8 - - + -
149A TYR* 4.8 1.8 - - + -
150A TYR* 1.3 75.5 - - - +
152A PHE* 1.3 62.5 + - - +
153A THR* 3.6 17.2 + - + -
159A VAL* 4.5 7.2 - - + -
170A LEU* 3.9 27.8 - - + -
171A SER 2.9 12.9 + - - +
172A VAL* 3.5 9.2 - - + +
173A LEU* 2.9 25.8 + - - +
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Residues in contact with PHE 152 (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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119A THR* 4.4 8.3 - - - -
120A VAL 2.9 17.0 + - - +
121A PHE* 3.4 41.3 - + + -
122A ALA* 2.9 26.7 + - - +
123A ILE* 3.7 2.8 - - - +
150A TYR* 3.9 23.1 - - + -
151A VAL* 1.3 71.6 - - - +
153A THR* 1.3 58.5 + - - +
173A LEU* 3.3 31.4 - - + -
175A VAL* 3.8 21.8 - - + -
199A ARG* 3.7 26.0 - - - -
200A PHE* 4.1 13.2 - + - -
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Residues in contact with THR 153 (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 ALA* 2.6 25.0 + - - -
123A ILE* 4.4 0.4 - - - -
127A VAL* 3.6 11.5 - - - +
130A LEU* 5.5 0.2 - - - -
151A VAL* 4.2 9.9 - - + +
152A PHE* 1.3 74.6 - - - +
154A ASP* 1.3 65.9 + - - +
155A GLN* 3.0 25.3 + - - +
156A PRO* 3.9 2.2 - - + +
159A VAL* 4.0 9.5 - - + +
172A VAL* 3.8 28.5 - - + -
173A LEU 3.0 5.4 + - - +
174A GLU* 3.2 9.7 - - - +
175A VAL* 2.9 28.5 + - - +
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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