Contacts of the strand formed by residues 156 - 160 (chain A) in PDB entry 1XAI
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 ALA 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A TYR* 4.1 2.5 - - - -
13A PRO* 3.3 28.7 - - + -
15A TYR* 4.7 3.6 - - + -
27A TYR* 3.6 26.0 - - + +
119A PHE 3.6 1.3 + - - +
120A ILE* 3.5 8.2 - - + +
121A GLN* 3.1 22.9 + - - +
154A PRO* 3.1 1.9 - - - +
155A THR* 1.3 84.6 - - - +
157A VAL* 1.3 66.3 + - - +
158A ILE* 4.7 7.0 - - + -
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Residues in contact with VAL 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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12A TYR* 3.7 26.7 - - + -
13A PRO 3.0 10.5 + - - +
14A ILE* 3.2 21.2 - - + -
15A TYR* 2.7 32.7 + - - -
121A GLN* 3.4 17.0 - - + +
123A PRO* 4.1 7.0 - - + -
132A SER* 3.6 41.5 - - - +
133A VAL* 5.0 1.8 - - + -
154A PRO* 3.9 6.7 - - + -
156A ALA* 1.3 79.9 - - - +
158A ILE* 1.3 62.8 + - - +
159A TYR* 4.0 2.2 - - + +
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Residues in contact with ILE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A TYR* 3.6 23.8 - - + -
20A ALA* 2.9 36.8 - - + +
21A ILE* 4.2 3.6 - - - +
23A TYR* 3.9 16.8 - - + +
24A ILE* 3.4 35.9 - - + -
27A TYR* 4.9 3.8 - - + -
120A ILE* 3.9 18.4 - - + -
121A GLN 2.6 13.3 + - - +
122A VAL* 3.4 25.8 - - + +
123A PRO* 3.5 2.8 - - - +
156A ALA* 4.7 10.3 - - + -
157A VAL* 1.3 78.5 - - - +
159A TYR* 1.3 57.8 + - - +
160A ASP 3.5 4.3 + - - +
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Residues in contact with TYR 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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14A ILE* 5.4 1.3 - - + -
15A TYR 2.7 21.1 + - - +
16A VAL* 3.4 19.8 - - + -
17A GLU 3.4 5.9 + - - +
20A ALA* 3.8 0.9 - - - -
123A PRO* 3.5 33.7 - - + -
124A THR 5.0 0.4 - - - -
125A THR 2.5 30.0 + - - -
126A ILE* 3.4 16.3 + - - -
128A ALA 5.1 0.2 - - - -
129A HIS* 3.3 30.5 - - + +
132A SER* 5.4 0.9 - - - -
157A VAL* 4.0 5.7 - - + -
158A ILE* 1.3 70.6 - - - +
160A ASP* 1.3 70.9 + - - +
161A LEU* 3.2 10.6 + - + +
164A LEU* 4.0 15.7 - - + +
214A ILE* 3.5 22.4 - - + +
218A ILE* 3.6 20.0 - - + -
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Residues in contact with ASP 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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17A GLU 3.2 4.9 - - - -
18A HIS 3.0 19.3 - - - +
19A GLY* 4.0 2.9 - - - -
20A ALA* 3.5 7.8 - - - +
21A ILE* 3.1 45.5 - - + +
49A LYS* 3.8 11.1 + - - -
123A PRO 4.5 2.6 + - - -
158A ILE* 3.5 6.2 + - + +
159A TYR* 1.3 77.4 - - - +
161A LEU* 1.3 56.1 + - - +
162A ASP* 3.0 25.2 + - - +
163A PHE* 3.3 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