Contacts of the strand formed by residues 58 - 64 (chain P) in PDB entry 1IJS
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 58 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53P PHE* 3.6 0.7 - - - -
54P LEU* 2.5 49.1 + - + +
55P GLU 3.5 16.4 - - - +
56P ASN* 2.6 38.5 + - + +
57P GLY* 1.3 79.8 - - - +
59P VAL* 1.3 55.1 + - - +
135P GLU* 5.3 2.9 - - - -
137P HIS* 4.1 31.0 - + - -
536P LYS* 3.9 31.4 - - + -
537P ALA 3.7 11.9 - - - -
538P LYS* 3.6 24.5 - - + +
539P LEU* 5.5 0.2 - - - +
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Residues in contact with VAL 59 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51P PHE* 4.2 6.5 - - + -
52P LYS 3.3 11.4 - - - +
53P PHE* 2.7 45.5 - - + -
54P LEU* 3.7 4.5 - - - -
58P TRP* 1.3 77.1 - - - +
60P TYR* 1.3 81.3 + - - +
61P ILE* 4.1 4.9 - - + -
133P MET* 3.7 24.2 - - + -
536P LYS* 3.5 12.0 - - - +
537P ALA 2.9 32.8 + - - +
539P LEU* 3.8 18.8 - - + -
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Residues in contact with TYR 60 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50P GLU 3.1 6.2 - - - +
51P PHE* 3.4 1.7 - - - -
52P LYS* 2.6 68.2 + - + +
54P LEU* 3.5 18.4 - - + -
59P VAL* 1.3 75.1 - - - +
61P ILE* 1.3 62.3 + - - +
62P THR* 3.6 25.5 + - - -
139P VAL* 5.3 5.4 - - + +
532P LYS* 6.3 1.3 - - - -
534P VAL* 4.3 19.8 - - + +
535P PHE 3.8 2.5 - - - -
536P LYS* 3.8 31.6 - - + -
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Residues in contact with ILE 61 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49P THR* 5.3 2.5 - - + -
50P GLU 3.4 3.6 - - - +
51P PHE* 3.5 31.0 - - + -
59P VAL* 4.1 2.4 - - + -
60P TYR* 1.3 71.6 - - - +
62P THR* 1.3 61.0 + - - +
63P ALA 4.7 2.5 - - - +
121P PHE* 3.9 20.9 - - + -
129P ILE* 3.8 13.0 - - + -
133P MET* 3.0 39.7 - - + -
136P LEU* 4.7 9.4 - - + -
534P VAL* 3.3 1.3 - - - -
535P PHE* 2.4 71.3 + - + +
537P ALA* 5.1 2.2 - - + +
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Residues in contact with THR 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P GLN 3.9 0.3 - - - +
49P THR* 5.5 0.2 - - - -
50P GLU* 3.2 49.0 + - - +
60P TYR* 3.6 27.9 + - - -
61P ILE* 1.3 73.3 - - - +
63P ALA* 1.3 59.1 + - - +
64P ASN* 3.8 14.7 + - - +
532P LYS* 3.3 44.0 - - + -
533P LEU 3.4 3.1 - - - -
534P VAL* 4.2 7.8 - - + +
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Residues in contact with ALA 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48P GLN 4.1 4.0 - - - -
49P THR* 4.8 5.4 - - + +
61P ILE 3.9 1.6 - - - -
62P THR* 1.3 73.4 - - - +
64P ASN* 1.3 60.6 + - - +
120P TRP* 3.4 40.0 - - + +
121P PHE* 4.1 22.4 - - + -
532P LYS* 3.3 2.1 - - - -
533P LEU* 2.7 45.0 + - + +
535P PHE* 4.6 0.7 - - + -
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Residues in contact with ASN 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46P ASN* 3.1 39.1 - - + +
47P ASN* 3.0 28.4 - - - +
48P GLN 3.3 11.2 + - - +
49P THR* 5.6 0.2 + - - -
50P GLU* 4.1 14.0 - - - +
62P THR* 3.8 14.5 - - - +
63P ALA* 1.3 72.9 + - - +
65P SER* 1.3 59.7 + - - +
120P TRP* 4.5 2.9 - - - +
530P LYS* 5.0 5.8 - - - +
531P GLY 2.8 9.1 + - - +
532P LYS* 3.2 41.6 - - - +
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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