Contacts of the strand formed by residues 20 - 25 (chain A) in PDB entry 1XBT
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 GLN 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A ARG 4.8 2.1 - - - +
19A GLY* 1.3 75.1 - - - +
21A ILE* 1.3 61.6 + - - +
22A GLN* 3.1 44.7 + - - +
43A PHE* 5.7 1.6 - - - -
113A ALA* 3.7 5.7 - - - +
117A LYS 3.0 7.8 + - - +
118A THR* 4.3 18.0 + - + +
119A VAL* 2.8 33.4 + - - +
144A GLU* 3.8 34.0 - - + +
145A SER* 4.4 4.8 - - - -
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Residues in contact with ILE 21 (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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20A GLN* 1.3 77.9 - - - +
22A GLN* 1.3 66.3 + - - +
23A VAL* 4.0 20.9 - - + -
109A CYS* 3.7 35.4 - - + +
110A GLU* 3.8 12.6 - - - +
113A ALA* 3.7 8.1 - - + -
119A VAL* 3.3 8.7 - - + +
121A VAL* 4.8 5.4 - - + -
139A LEU* 4.5 13.9 - - + -
142A LEU* 3.8 14.8 - - + +
143A ALA* 3.6 14.1 - - + +
144A GLU* 3.0 32.8 + - - +
145A SER 3.4 4.2 + - - -
186C ARG* 3.5 21.3 - - - +
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Residues in contact with GLN 22 (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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20A GLN* 3.1 40.1 + - + +
21A ILE* 1.3 72.7 - - - +
23A VAL* 1.3 64.2 + - - +
39A ARG* 2.9 40.6 + - - +
42A ARG* 5.7 1.5 + - - +
43A PHE* 5.0 8.3 - - - -
118A THR* 4.3 11.3 - - + +
119A VAL 2.8 12.7 + - - +
120A ILE* 3.4 18.7 - - + +
121A VAL* 2.8 28.4 + - - +
145A SER* 3.4 17.7 - - - -
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Residues in contact with VAL 23 (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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21A ILE* 4.0 11.2 - - + -
22A GLN* 1.3 79.2 - - - +
24A ILE* 1.3 65.9 + - - +
25A LEU* 3.7 35.4 - - + -
39A ARG* 4.8 2.0 + - - +
121A VAL* 3.5 8.5 - - + +
123A ALA* 5.7 0.2 - - + -
136A ILE* 4.2 11.0 - - + -
139A LEU* 4.1 23.8 - - + -
140A VAL* 5.4 3.1 - - + -
143A ALA* 4.0 19.7 - - + -
145A SER* 2.8 14.1 + - - +
146A VAL* 3.4 10.4 - - + -
147A VAL* 3.0 27.7 + - - +
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Residues in contact with ILE 24 (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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23A VAL* 1.3 73.8 - - - +
25A LEU* 1.3 63.5 + - - +
32A LYS* 4.0 13.9 - - - +
35A GLU* 3.8 23.6 - - + -
36A LEU* 3.8 20.0 - - + +
39A ARG* 3.7 26.0 - - - +
120A ILE* 3.8 27.4 - - + -
121A VAL 2.7 14.4 + - - +
122A ALA* 4.2 2.7 - - - -
123A ALA 2.9 27.2 + - - +
147A VAL* 3.7 6.5 - - + -
149A LEU* 3.9 32.5 - - + -
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Residues in contact with LEU 25 (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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23A VAL* 3.7 23.3 - - + -
24A ILE* 1.3 75.3 - - - +
26A GLY* 1.3 54.6 + - - +
32A LYS* 3.8 4.2 - - - +
123A ALA* 3.2 18.8 - - + +
125A ASP* 3.9 23.6 - - + +
136A ILE* 3.8 20.6 - - + -
137A LEU* 4.4 8.3 - - + -
140A VAL* 4.5 4.9 - - + -
146A VAL* 4.0 24.0 - - + -
147A VAL 2.7 13.6 + - - +
148A LYS* 3.9 9.0 - - + -
149A LEU* 2.7 35.6 + - - +
140C VAL* 4.1 25.1 - - + -
146C VAL* 5.8 1.1 - - + -
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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