Contacts of the strand formed by residues 20 - 25 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 4.3 0.4 - - - +
18C ARG 4.8 2.6 - - - +
19C GLY* 1.3 75.3 - - - +
21C ILE* 1.3 62.5 + - - +
22C GLN* 3.1 38.3 + - + +
43C PHE* 4.9 5.5 - - - -
113C ALA* 3.8 6.0 - - - +
117C LYS 3.1 6.6 + - - +
118C THR* 3.5 29.7 + - + +
119C VAL* 2.8 31.2 + - - +
144C GLU* 3.4 28.7 - - + +
145C SER* 5.4 1.8 - - - -
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Residues in contact with ILE 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A ARG* 3.5 16.6 - - - +
20C GLN* 1.3 78.1 - - - +
22C GLN* 1.3 65.7 + - - +
23C VAL* 4.0 22.0 - - + -
109C CYS* 3.8 33.7 - - + +
110C GLU* 3.8 15.5 - - - +
113C ALA* 3.7 10.8 - - + -
119C VAL* 3.3 9.2 - - + +
121C VAL* 4.8 3.1 - - + -
139C LEU* 4.2 22.7 - - + -
142C LEU* 3.8 8.7 - - + +
143C ALA* 3.6 9.5 - - + +
144C GLU* 2.9 36.1 + - - +
145C SER 3.5 4.3 + - - -
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLN* 3.1 38.5 + - + +
21C ILE* 1.3 79.0 - - - +
23C VAL* 1.3 63.7 + - - +
39C ARG* 2.9 42.2 + - - +
42C ARG* 5.8 1.9 + - - +
43C PHE* 5.0 7.9 - - - -
118C THR* 4.4 6.0 - - - +
119C VAL 2.8 12.6 + - - +
120C ILE* 3.5 19.2 - - + +
121C VAL* 2.8 27.7 + - - +
145C SER* 3.4 17.0 - - - -
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Residues in contact with VAL 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 4.0 2.2 - - + -
22C GLN* 1.3 79.4 - - - +
24C ILE* 1.3 64.1 + - - +
25C LEU* 3.8 33.9 - - + -
39C ARG* 4.9 2.1 + - - -
121C VAL* 3.5 10.8 - - + +
123C ALA* 5.5 0.2 - - + -
136C ILE* 5.0 9.2 - - + +
139C LEU* 4.0 31.2 - - + +
140C VAL* 5.1 4.7 - - + +
143C ALA* 3.8 21.3 - - + -
145C SER* 2.8 12.8 + - - +
146C VAL* 3.5 11.4 - - + -
147C VAL* 3.1 27.2 + - - +
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Residues in contact with ILE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C VAL* 1.3 75.2 - - - +
25C LEU* 1.3 63.0 + - - +
32C LYS* 3.8 14.0 - - + +
35C GLU* 3.9 13.0 - - + -
36C LEU* 3.8 36.8 - - + +
39C ARG* 3.8 24.9 - - - +
120C ILE* 3.8 19.3 - - + -
121C VAL 2.7 14.8 + - - +
122C ALA* 3.4 2.6 - - - -
123C ALA 2.9 27.4 + - - +
147C VAL* 3.8 5.8 - - + -
149C LEU* 3.6 34.8 - - + -
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 3.8 28.0 - - + -
146A VAL* 5.7 1.3 - - + -
23C VAL* 3.8 23.3 - - + -
24C ILE* 1.3 75.2 - - - +
26C GLY* 1.3 54.2 + - - +
32C LYS* 3.7 4.9 - - - +
123C ALA* 3.3 23.3 - - + +
125C ASP* 3.9 20.4 - - + -
136C ILE* 4.4 10.5 - - + +
137C LEU* 4.5 2.7 - - + -
140C VAL* 4.5 10.1 - - + -
146C VAL* 4.1 22.0 - - + -
147C VAL 2.8 13.7 + - - +
148C LYS* 4.0 12.3 - - + -
149C LEU* 2.7 35.6 + - - +
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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