Contacts of the strand formed by residues 20 - 26 (chain A) in PDB entry 1K4R
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 ARG 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 THR* 3.4 12.5 - - - +
19A THR* 1.3 87.5 - - + +
21A VAL* 1.3 73.1 + - - +
22A THR* 5.6 1.3 - - - +
171A LYS* 5.6 7.0 - - - +
185A LEU* 4.5 13.3 - - - +
187A ARG* 5.8 0.2 - - - +
291A GLU* 2.9 44.1 + - + +
292A VAL 3.4 11.9 - - - +
293A GLY* 4.9 7.9 - - - -
295A GLU* 5.2 4.0 - - - -
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Residues in contact with VAL 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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12A VAL* 3.4 21.5 - - + -
14A GLY* 5.0 6.5 - - - +
18A THR* 4.1 14.4 - - + -
20A ARG* 1.3 81.1 - - - +
22A THR* 1.3 66.2 + - - +
23A LEU* 3.4 29.8 - - + -
33A ILE* 4.7 10.3 - - + -
290A CYS 3.8 0.7 - - - +
291A GLU* 3.3 2.3 - - - -
292A VAL* 2.7 47.0 + - + +
294A LEU* 4.1 21.5 - - + -
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Residues in contact with THR 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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12A VAL* 5.5 1.7 - - - +
20A ARG* 5.6 1.7 - - - +
21A VAL* 1.3 75.0 - - - +
23A LEU* 1.3 71.8 + - - +
24A VAL* 6.0 1.6 - - + -
289A THR* 5.0 9.9 - - - -
290A CYS 3.3 10.5 - - - +
291A GLU* 3.9 22.0 + - + +
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Residues in contact with LEU 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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12A VAL* 3.5 30.3 - - + -
21A VAL* 3.4 28.9 - - + -
22A THR* 1.3 75.2 - - - +
24A VAL* 1.3 65.1 + - - +
25A LEU* 3.8 30.8 + - + +
31A VAL* 3.9 13.5 - - + -
33A ILE* 3.9 13.7 - - + -
43A VAL* 4.4 9.4 - - + -
289A THR* 3.1 6.3 - - - -
290A CYS* 2.9 34.6 + - + +
292A VAL* 3.8 26.0 - - + -
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Residues in contact with VAL 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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10A ASP* 5.2 4.3 - - - +
22A THR* 6.0 2.5 - - + -
23A LEU* 1.3 73.1 - - - +
25A LEU* 1.3 68.2 + - - +
26A GLU* 3.9 9.7 + - - +
31A VAL* 4.9 6.2 - - - +
287A HIS* 4.5 18.6 - - + -
288A VAL 3.6 7.0 - - - +
289A THR* 3.4 25.8 - - + -
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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 LEU* 3.8 22.0 - - + +
24A VAL* 1.3 72.7 - - - +
26A GLU* 1.3 59.9 + - - +
31A VAL* 3.5 30.3 - - + -
43A VAL* 4.0 31.2 - - + +
44A TRP* 4.4 2.7 - - - -
45A LEU* 3.8 21.6 - - + +
141A VAL* 4.0 15.5 - - + -
287A HIS* 3.1 4.7 - - - +
288A VAL* 2.9 38.8 + - + +
290A CYS* 3.8 29.4 - - + -
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Residues in contact with GLU 26 (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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8A ASN* 3.2 31.9 + - - +
10A ASP* 5.1 8.0 - - - +
24A VAL* 3.9 8.9 + - + +
25A LEU* 1.3 76.2 - - - +
27A LEU* 1.3 64.4 + - - +
28A GLY 3.3 0.3 + - - -
29A GLY* 2.9 31.6 + - - +
45A LEU* 4.2 10.0 + - - +
286A GLY 3.5 10.5 - - - +
287A HIS* 4.1 9.0 - - + +
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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