Contacts of the strand formed by residues 53 - 60 (chain L) in PDB entry 1IBL
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 53 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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521A G 3.0 49.9 + - - -
522A C 3.7 7.8 + - - +
523A A 3.1 17.9 - - - +
529A G 4.9 0.2 - - - +
42L THR* 3.3 5.9 - - - -
43L VAL* 2.7 43.6 + - + +
45L PRO* 3.9 17.9 - - - +
49L ASN* 4.6 1.8 + - - +
51L ALA* 3.9 11.3 - - - +
52L LEU* 1.3 74.5 - - - +
54L LYS* 1.3 62.6 + - - +
55L VAL* 3.8 0.4 + - + -
69L TYR* 3.2 36.0 + - + +
92L ASP* 2.6 34.8 + - - +
93L LEU* 3.3 29.6 - - + -
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Residues in contact with LYS 54 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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520A A 3.8 14.6 + - - -
521A G 3.1 35.6 + - - +
41L ARG 4.1 4.7 - - - +
42L THR* 4.8 7.2 + - - +
52L LEU* 2.7 24.2 + - - +
53L ARG* 1.3 73.3 - - - +
55L VAL* 1.3 60.3 + - - +
69L TYR* 3.1 28.5 + - - -
70L ILE* 3.3 30.3 + - + +
73L GLU 5.4 1.8 - - - +
75L HIS* 3.4 28.7 - - + +
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Residues in contact with VAL 55 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L VAL* 3.4 8.8 - - - +
41L ARG* 3.2 49.9 + - - +
43L VAL* 4.7 16.6 - - + -
53L ARG 3.8 3.1 + - - +
54L LYS* 1.3 82.5 - - - +
56L ALA* 1.3 68.1 + - - +
57L LYS* 4.3 0.7 - - - +
67L THR* 3.2 30.3 - - + -
68L ALA 3.5 9.6 - - - +
69L TYR* 4.1 13.5 - - + -
70L ILE* 4.1 5.7 - - - +
93L LEU* 4.2 14.6 - - + -
96L VAL* 4.3 6.3 - - + -
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Residues in contact with ALA 56 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37L CYS* 4.3 11.0 - - - -
39L VAL 3.6 12.1 - - - +
40L VAL* 4.8 2.7 - - + -
55L VAL* 1.3 79.9 - - - +
57L LYS* 1.3 60.6 + - - +
58L VAL* 3.5 9.7 + - + +
67L THR* 3.1 3.3 - - - -
68L ALA 2.6 45.5 + - - +
70L ILE* 4.4 6.5 - - + -
77L LEU* 5.0 0.7 - - + -
100L ILE* 3.9 22.7 - - + -
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Residues in contact with LYS 57 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1411A C 3.7 12.4 + - - -
1412A C 3.3 30.7 - - - +
37L CYS* 3.6 1.2 - - - -
38L THR* 2.8 39.3 + - + -
39L VAL* 3.3 29.7 + - + -
41L ARG* 2.5 51.6 - - - +
55L VAL* 4.3 0.8 - - - +
56L ALA* 1.3 68.6 - - - +
58L VAL* 1.3 56.8 + - - +
65L GLU 5.7 1.8 - - - +
66L VAL 3.7 3.8 - - - -
67L THR* 3.4 34.6 + - - +
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Residues in contact with VAL 58 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35L GLY* 3.7 13.7 - - - +
36L VAL 3.3 26.0 - - - +
37L CYS* 4.7 2.2 - - - -
38L THR* 4.8 0.7 - - - -
56L ALA* 3.8 25.6 - - + +
57L LYS* 1.3 77.5 - - - +
59L ARG* 1.3 62.9 + - - +
60L LEU* 3.3 5.4 - - + +
65L GLU* 3.1 3.2 - - - -
66L VAL 2.6 45.2 + - - +
68L ALA* 4.0 15.3 - - + -
83L VAL* 4.2 17.3 - - + -
85L ILE* 4.0 18.4 - - + -
100L ILE* 4.5 0.7 - - + -
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Residues in contact with ARG 59 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L GLY* 3.3 3.5 - - - -
36L VAL* 2.9 35.2 + - + +
38L THR* 4.2 24.9 + - - +
57L LYS 4.2 0.6 + - - -
58L VAL* 1.3 69.1 - - - +
60L LEU* 1.3 66.2 + - - +
63L GLY* 6.3 0.2 - - - -
64L TYR 3.0 12.3 - - - +
65L GLU* 3.4 32.6 + - + +
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Residues in contact with LEU 60 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25L PRO 6.2 0.2 - - - +
26L ALA* 6.1 3.4 - - - -
33L ARG* 3.7 19.7 - - + +
34L ARG 3.6 21.1 - - - +
35L GLY* 4.3 2.5 - - - +
58L VAL* 3.3 13.7 - - + +
59L ARG* 1.3 78.1 - - - +
61L THR* 1.3 62.3 + - - +
62L SER* 3.0 21.3 - - - +
63L GLY* 3.2 11.6 + - - -
64L TYR* 2.5 29.2 + - + +
66L VAL* 3.2 37.2 - - + +
85L ILE* 3.7 22.9 - - + -
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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