Contacts of the strand formed by residues 59 - 64 (chain A) in PDB entry 1SIW
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 TRP 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A VAL 3.5 0.5 - - - +
46A ARG* 3.3 0.7 - - - -
47A SER 2.7 38.5 + - - +
48A THR* 4.5 1.8 - - - -
49A HIS* 3.1 29.8 + + - +
57A CYS* 3.2 30.7 - - - +
58A SER* 1.3 73.6 - - - +
60A LYS* 1.3 61.0 + - - +
61A ILE* 3.7 13.2 - - + -
71A GLU* 3.5 28.0 - - + -
72A THR* 3.4 24.9 - - - -
73A GLN* 3.4 34.1 - - + -
74A GLN* 3.2 14.5 + - - -
91A GLY* 3.7 10.5 - - - -
92A CYS 4.0 4.3 - - - -
96A ALA* 3.6 32.3 - - + -
792A TYR* 4.9 1.1 - - - +
1248A SF4 3.3 29.0 - - - -
21B THR* 4.7 0.9 - - + -
25B THR* 4.8 1.3 - - + -
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Residues in contact with LYS 60 (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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44A ILE* 3.5 27.2 - - + +
45A VAL 3.7 3.6 - - - -
59A TRP* 1.3 72.0 - - - +
61A ILE* 1.3 60.8 + - - +
62A TYR* 3.4 19.9 + - + +
71A GLU* 3.1 26.0 - - - +
72A THR* 2.8 28.9 + - - +
73A GLN 4.0 12.9 + - - +
74A GLN* 3.5 33.0 - - + +
75A THR* 5.1 5.4 + - - +
250B ARG* 4.8 5.3 - - - +
261B GLU* 4.5 17.6 + - - -
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Residues in contact with ILE 61 (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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43A LYS 3.7 0.3 - - - +
44A ILE* 3.2 5.8 - - - -
45A VAL* 2.7 43.2 + - + +
47A SER* 3.9 17.0 - - - -
59A TRP* 3.5 29.2 - - + +
60A LYS* 1.3 77.3 - - - +
62A TYR* 1.3 64.0 + - - +
63A VAL* 3.8 2.1 + - - +
68A VAL* 4.0 26.0 - - + -
70A TRP 4.0 2.9 - - - +
71A GLU* 4.5 1.6 - - + -
792A TYR* 3.7 36.3 - - + +
812A ALA* 3.6 28.0 - - + -
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Residues in contact with TYR 62 (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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39A TRP* 3.6 21.2 - + - -
41A HIS* 3.5 40.4 - + + -
43A LYS 3.7 4.0 - - - +
44A ILE* 3.5 21.7 - - + +
60A LYS* 3.4 30.1 + - + +
61A ILE* 1.3 73.3 - - - +
63A VAL* 1.3 61.3 + - - +
68A VAL* 3.5 5.5 - - - +
69A THR* 2.9 30.0 + - - +
70A TRP* 2.9 61.7 + + + +
71A GLU* 3.9 0.2 - - - -
72A THR* 2.7 33.8 + - + -
250B ARG* 4.8 5.2 + - - -
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Residues in contact with VAL 63 (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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41A HIS* 3.4 3.4 - - - +
42A ASP* 2.7 40.3 + - + +
43A LYS* 3.1 41.4 + - + -
45A VAL* 5.0 0.2 - - + -
61A ILE* 4.5 3.6 - - + +
62A TYR* 1.3 75.7 - - - +
64A LYS* 1.3 58.1 + - - +
66A GLY* 3.8 12.1 - - - -
67A LEU 3.1 25.4 - - - +
68A VAL* 4.3 3.8 - - + -
812A ALA* 3.9 23.3 - - + -
813A VAL* 4.1 13.5 - - + -
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Residues in contact with LYS 64 (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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37A GLN 2.7 28.5 + - - -
38A ARG* 3.1 33.3 + - - +
40A GLN* 2.7 26.0 + - - +
41A HIS* 4.2 8.1 - - + -
42A ASP* 3.5 7.0 - - - +
62A TYR 4.1 0.4 - - - -
63A VAL* 1.3 74.8 - - - +
65A ASN* 1.3 87.6 + - + +
66A GLY 3.0 0.7 - - - -
67A LEU* 2.8 22.2 + - - +
69A THR* 3.8 23.6 - - + +
70A TRP* 4.2 13.0 - - + -
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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