Contacts of the strand formed by residues 23 - 31 (chain A) in PDB entry 6YBX
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 ALA 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ALA 3.9 1.3 - - - -
19A LYS* 5.6 0.5 - - - +
22A ALA* 1.3 83.4 - - - +
24A LEU* 1.3 64.7 + - - +
25A ASP 3.8 17.7 + - - +
26A ALA 4.4 2.7 - - - +
27A GLY* 3.8 9.0 - - - +
76A ARG* 5.5 0.9 - - + +
77A CYS 3.2 24.9 - - - +
78A LYS* 3.7 16.8 - - + +
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Residues in contact with LEU 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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17A ALA* 3.0 25.7 + - + +
18A SER 3.8 28.0 - - - +
19A LYS* 4.2 21.1 - - + -
22A ALA 3.8 0.2 + - - -
23A ALA* 1.3 74.9 - - - +
25A ASP* 1.3 72.7 + - - +
27A GLY* 2.9 14.4 + - - -
37A TRP* 5.2 0.5 - - - -
39A ILE* 4.8 0.8 - - + +
41A VAL* 4.4 24.9 - - + -
42A GLU 5.7 0.9 - - - +
45A THR* 4.2 16.2 - - + +
48A GLY* 4.2 3.6 - - - -
49A LYS 4.6 0.2 - - - +
90A PHE* 3.7 34.5 - - + -
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Residues in contact with ASP 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 ALA* 3.8 11.6 + - - +
24A LEU* 1.3 75.7 - - - +
26A ALA* 1.3 79.2 + - - +
37A TRP* 4.4 3.8 + - - -
38A THR 4.6 1.2 - - - +
39A ILE* 3.4 29.5 - - + +
40A ASN* 2.9 42.3 + - - +
41A VAL* 5.9 0.2 - - - +
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Residues in contact with ALA 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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23A ALA* 4.4 3.9 - - - +
25A ASP* 1.3 88.6 + - - +
27A GLY* 1.3 55.8 + - - +
28A GLY 3.3 9.0 + - - +
29A ARG* 6.3 0.9 - - + -
37A TRP* 4.1 15.8 - - + +
76A ARG* 3.1 47.1 - - - +
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Residues in contact with GLY 27 (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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16A ALA* 3.3 4.0 - - - -
17A ALA 3.0 34.4 + - - +
23A ALA* 3.8 3.4 - - - -
24A LEU 2.9 17.4 + - - -
25A ASP 3.2 0.2 - - - -
26A ALA* 1.3 76.4 - - - +
28A GLY* 1.3 55.0 + - - +
37A TRP* 4.1 4.9 - - - -
77A CYS* 3.3 30.4 + - - +
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Residues in contact with GLY 28 (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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15A ALA 3.1 14.6 - - - -
26A ALA* 3.3 8.6 + - - +
27A GLY* 1.3 79.4 - - - +
29A ARG* 1.3 66.3 + - - +
37A TRP* 3.6 11.4 - - - -
53A ARG* 3.7 0.2 - - - -
75A LEU* 3.4 21.4 - - - +
76A ARG* 3.9 14.7 + - - +
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Residues in contact with ARG 29 (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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14A TRP* 3.4 6.8 - - - -
15A ALA* 2.9 31.8 + - - +
26A ALA* 6.3 0.4 - - + -
28A GLY* 1.3 76.5 - - - +
30A GLN* 1.3 86.9 + - - +
31A LEU* 3.4 16.3 + - + +
35A GLU* 3.3 14.8 + - - -
36A SER 4.0 3.0 + - - -
37A TRP* 3.8 46.4 - - + +
53A ARG* 4.1 2.2 - - - +
75A LEU* 4.4 7.4 - - + -
301A TLA 2.8 48.4 + - - -
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Residues in contact with GLN 30 (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 THR* 3.6 19.9 + - + +
13A VAL 3.8 0.7 - - - -
14A TRP* 3.5 37.5 + - - +
29A ARG* 1.3 101.5 + - - +
31A LEU* 1.3 61.1 + - - +
32A ASN* 3.0 30.1 + - - +
35A GLU* 3.7 2.9 - - - +
75A LEU* 4.4 4.1 - - + +
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Residues in contact with LEU 31 (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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5A ILE* 3.9 35.4 - - + +
7A ASN* 3.0 41.9 + - + +
12A THR* 3.5 1.4 - - - -
13A VAL* 2.8 28.2 + - + +
15A ALA* 3.9 14.1 - - + -
29A ARG* 3.4 30.7 - - - +
30A GLN* 1.3 72.8 - - - +
32A ASN* 1.3 63.6 + - - +
35A GLU* 3.5 19.1 - - + +
37A TRP* 3.8 20.4 - - + +
203A PHE* 4.2 5.2 - - + -
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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