Contacts of the strand formed by residues 20 - 25 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E ARG 4.8 2.1 - - - +
19E GLY* 1.3 75.1 - - - +
21E ILE* 1.3 61.8 + - - +
22E GLN* 2.8 40.2 + - - +
43E PHE* 5.5 2.9 - - - -
113E ALA* 3.7 5.5 - - - +
117E LYS 3.1 7.6 + - - +
118E THR* 3.9 20.2 + - + +
119E VAL* 2.8 31.3 + - - +
144E GLU* 3.1 34.3 - - + +
145E SER* 5.0 4.2 - - - -
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Residues in contact with ILE 21 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLN* 1.3 78.3 - - - +
22E GLN* 1.3 66.0 + - - +
23E VAL* 4.2 12.6 - - + -
109E CYS* 3.4 40.6 - - + +
110E GLU* 3.8 10.1 - - - +
113E ALA* 3.6 11.0 - - + -
119E VAL* 3.3 8.5 - - + +
121E VAL* 4.9 3.1 - - + -
139E LEU* 4.4 21.3 - - + -
142E LEU* 4.2 6.7 - - + +
143E ALA* 3.4 21.1 - - + +
144E GLU* 2.8 40.8 + - - +
145E SER 3.5 2.8 + - - -
186G ARG* 3.7 14.8 - - - +
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Residues in contact with GLN 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20E GLN* 2.8 39.8 + - + +
21E ILE* 1.3 74.5 - - - +
23E VAL* 1.3 64.1 + - - +
39E ARG* 2.8 43.1 + - - +
42E ARG* 5.8 1.5 + - - +
43E PHE* 4.9 8.9 - - - -
118E THR* 4.2 11.9 - - + +
119E VAL 2.8 13.3 + - - +
120E ILE* 3.5 18.7 - - + +
121E VAL* 2.8 29.5 + - - +
145E SER* 3.5 15.3 - - - +
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Residues in contact with VAL 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E ILE* 4.2 2.0 - - + -
22E GLN* 1.3 78.8 - - - +
24E ILE* 1.3 64.9 + - - +
25E LEU* 3.6 35.0 - - + -
39E ARG* 5.0 1.1 + - - -
121E VAL* 3.5 7.6 - - + +
123E ALA* 5.7 0.2 - - + -
136E ILE* 4.3 10.8 - - + -
139E LEU* 3.9 32.1 - - + +
140E VAL* 5.2 4.0 - - + +
143E ALA* 3.9 20.2 - - + -
145E SER* 2.8 15.5 + - - +
146E VAL* 3.5 11.0 - - + -
147E VAL* 3.0 27.5 + - - +
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Residues in contact with ILE 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E VAL* 1.3 74.5 - - - +
25E LEU* 1.3 62.5 + - - +
32E LYS* 4.0 17.3 - - + +
35E GLU* 3.7 12.3 - - + -
36E LEU* 3.7 36.3 - - + +
39E ARG* 3.7 31.2 - - - +
120E ILE* 3.9 15.7 - - + -
121E VAL 2.7 13.9 + - - +
122E ALA* 4.1 1.8 - - - -
123E ALA 2.9 27.4 + - - +
147E VAL* 3.8 4.9 - - + -
149E LEU* 3.8 31.9 - - + -
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Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23E VAL* 3.6 27.8 - - + -
24E ILE* 1.3 75.9 - - - +
26E GLY* 1.3 54.8 + - - +
32E LYS* 3.8 5.4 - - - +
123E ALA* 3.3 16.4 - - + +
125E ASP* 4.0 28.0 - - + +
136E ILE* 3.7 20.6 - - + -
137E LEU* 4.3 8.7 - - + -
140E VAL* 4.6 4.7 - - + -
146E VAL* 4.2 17.3 - - + -
147E VAL 2.8 15.0 + - - +
148E LYS* 3.9 8.7 - - + -
149E LEU* 2.7 35.8 + - - +
140G VAL* 4.0 17.5 - - + -
146G VAL* 5.8 0.9 - - + -
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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