Contacts of the strand formed by residues 66 - 71 (chain A) in PDB entry 2RD1
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 VAL 66 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A MSE 4.0 18.4 - - + -
27A THR 3.8 1.8 - - - -
28A THR* 4.5 0.7 - - - +
29A LYS* 5.5 0.2 - - - -
49A THR* 4.5 7.0 - - + +
61A ILE* 4.0 22.4 - - + -
62A ASN 3.9 11.9 - - - +
63A SER* 3.8 18.0 - - - +
64A ASN 3.2 7.1 - - - +
65A ASP* 1.3 78.8 - - - +
67A ALA* 1.3 64.7 + - - +
68A GLN 3.9 10.3 - - - +
69A LEU* 3.8 14.4 - - + -
29B LYS* 3.0 38.0 - - - +
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Residues in contact with ALA 67 (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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27A THR* 2.6 29.0 + - + +
28A THR 4.0 12.3 - - - +
29A LYS* 4.2 1.1 - - - +
65A ASP 3.8 2.6 + - - -
66A VAL* 1.3 74.4 - - - +
68A GLN* 1.3 69.6 + - + +
29B LYS* 3.8 11.0 - - - +
67B ALA* 4.1 10.7 - - - +
67C ALA 4.2 19.3 - - - +
68C GLN* 4.3 7.4 - - + +
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Residues in contact with GLN 68 (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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25A VAL 3.7 1.1 - - - +
26A MSE 3.3 4.3 - - - -
27A THR* 2.8 41.0 + - - +
66A VAL* 3.9 2.8 - - - +
67A ALA* 1.3 89.3 - - + +
69A LEU* 1.3 61.9 + - - +
70A ILE* 3.9 18.4 - - + +
27B THR* 4.7 9.5 - - - -
28B THR 3.3 20.8 + - - +
29B LYS* 3.3 18.2 - - - +
31B GLY* 3.9 15.8 - - - -
67B ALA* 4.1 12.2 - - + +
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Residues in contact with LEU 69 (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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24A TYR* 4.4 15.3 - - + -
25A VAL 3.6 3.8 - - - +
26A MSE 3.5 39.0 - - + -
39A LYS* 4.4 12.6 - - + -
40A PRO* 3.5 41.7 - - + +
49A THR* 5.0 4.3 - - + -
66A VAL* 3.8 7.9 - - + -
68A GLN* 1.3 70.9 - - - +
70A ILE* 1.3 60.6 + - - +
71A LYS 4.2 0.7 + - - -
29B LYS* 2.7 35.9 + - + +
30B ASN* 3.2 23.5 - - + +
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Residues in contact with ILE 70 (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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24A TYR* 3.3 3.8 - - - -
25A VAL* 2.7 47.7 + - + +
27A THR* 5.9 1.1 - - - +
68A GLN* 3.9 22.4 - - + +
69A LEU* 1.3 79.5 - - - +
71A LYS* 1.3 75.4 + - - +
72A ALA* 3.3 1.4 + - - -
73A ASP* 5.8 1.8 - - - +
29B LYS 4.2 2.5 - - - +
30B ASN 3.7 21.8 - - - +
31B GLY* 3.8 17.9 - - - +
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Residues in contact with LYS 71 (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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22A THR 5.3 7.4 - - - +
23A ASN 3.8 4.3 - - - +
24A TYR* 3.1 52.1 - - + +
70A ILE* 1.3 81.7 - - - +
72A ALA* 1.3 74.7 + - - +
73A ASP* 3.7 8.8 + - - +
30B ASN 4.9 2.4 + - - -
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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