Contacts of the strand formed by residues 20 - 25 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18D ARG* 4.8 2.2 - - + +
19D GLY* 1.3 75.5 - - - +
21D ILE* 1.3 64.9 + - - +
22D GLN* 3.2 38.9 + - - +
43D PHE* 5.3 2.9 - - - -
113D ALA* 3.8 7.5 - - - +
117D LYS 3.0 6.5 + - - +
118D THR* 3.9 21.4 + - + +
119D VAL* 2.8 27.8 + - - +
144D GLU* 3.2 33.2 - - + +
145D SER* 4.8 5.1 - - - -
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Residues in contact with ILE 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ARG* 3.6 19.1 - - - +
20D GLN* 1.3 76.7 - - - +
22D GLN* 1.3 65.1 + - - +
23D VAL* 3.9 22.2 - - + -
109D CYS* 3.6 38.6 - - + +
110D GLU* 3.8 13.5 - - + +
113D ALA* 3.7 8.3 - - + -
119D VAL* 3.3 8.1 - - + +
121D VAL* 5.0 2.9 - - + -
139D LEU* 4.4 15.5 - - + -
142D LEU* 4.0 10.8 - - + +
143D ALA* 3.6 10.9 - - + +
144D GLU* 3.0 38.0 + - - +
145D SER 3.4 4.9 + - - -
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Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20D GLN* 3.2 34.3 + - + +
21D ILE* 1.3 76.9 - - - +
23D VAL* 1.3 66.2 + - - +
39D ARG* 2.9 40.3 + - - +
42D ARG* 5.8 1.1 + - - +
43D PHE* 5.0 7.5 - - - -
118D THR* 4.1 10.5 - - - +
119D VAL 2.8 13.3 + - - +
120D ILE* 3.4 16.8 - - + +
121D VAL* 2.8 27.7 + - - +
145D SER* 3.5 22.7 - - - +
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Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D ILE* 3.9 11.0 - - + -
22D GLN* 1.3 79.4 - - - +
24D ILE* 1.3 61.9 + - - +
25D LEU* 3.6 35.2 - - + -
39D ARG* 4.9 1.6 + - - +
121D VAL* 3.5 7.0 - - + +
136D ILE* 4.3 10.8 - - + -
139D LEU* 3.8 30.7 - - + -
140D VAL* 5.2 4.0 - - + -
143D ALA* 3.9 12.3 - - + -
145D SER* 2.8 13.6 + - - +
146D VAL* 3.5 12.2 - - + -
147D VAL* 3.0 29.1 + - - +
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Residues in contact with ILE 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D VAL* 1.3 74.3 - - - +
25D LEU* 1.3 63.6 + - - +
32D LYS* 4.0 14.6 - - + +
35D GLU* 4.0 6.7 - - + -
36D LEU* 3.8 30.5 - - + +
39D ARG* 3.9 29.2 - - - +
120D ILE* 3.8 26.5 - - + -
121D VAL 2.7 14.5 + - - +
122D ALA* 3.4 4.6 - - + -
123D ALA 2.9 28.4 + - - +
147D VAL* 3.8 7.6 - - + -
149D LEU* 3.7 33.7 - - + -
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B VAL* 4.0 17.0 - - + -
146B VAL* 5.7 1.1 - - + -
23D VAL* 3.6 27.4 - - + -
24D ILE* 1.3 76.1 - - - +
26D GLY* 1.3 54.3 + - - +
32D LYS* 3.7 6.3 - - - +
123D ALA 3.3 15.7 - - - +
125D ASP* 3.8 31.2 - - + +
136D ILE* 4.0 18.6 - - + -
137D LEU* 4.4 7.9 - - + -
140D VAL* 4.6 6.7 - - + -
146D VAL* 4.3 18.4 - - + -
147D VAL 2.8 14.7 + - - +
148D LYS* 3.9 9.0 - - + -
149D LEU* 2.7 35.8 + - - +
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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