Contacts of the strand formed by residues 18 - 25 (chain L) in PDB entry 3IT8
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 ASP 18 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8L THR 3.6 0.6 - - - +
9L VAL* 2.9 7.4 - - - +
10L THR* 2.8 38.1 + - - +
12L LYS* 2.9 41.1 - - + +
16L LEU* 4.0 1.9 + - - -
17L TYR* 1.3 75.2 - - - +
19L GLY* 1.3 60.4 + - - +
20L VAL* 5.9 2.5 - - + -
35L TYR 4.7 3.3 - - - +
37L HIS* 3.0 26.1 + - - -
70L TYR* 4.0 1.6 - - - -
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Residues in contact with GLY 19 (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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8L THR 3.2 7.6 - - - -
9L VAL* 4.2 0.4 - - - -
18L ASP* 1.3 77.5 + - - +
20L VAL* 1.3 64.3 + - - +
34L SER* 3.1 5.0 - - - -
35L TYR* 2.9 29.8 + - - +
66L PHE* 3.9 7.4 - - - -
70L TYR* 3.8 24.9 - - - -
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Residues in contact with VAL 20 (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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6L ASN 3.7 1.0 - - - +
7L TYR* 3.5 2.3 - - - -
8L THR* 2.8 51.2 + - + +
10L THR* 5.7 2.0 - - - +
18L ASP* 5.9 2.0 - - + -
19L GLY* 1.3 79.0 - - - +
21L PHE* 1.3 62.7 + - - +
22L TYR* 4.3 24.5 - - + +
32L LYS* 4.5 14.4 - - - -
33L ILE 3.1 10.3 - - - +
34L SER* 4.0 11.9 - - - -
66L PHE* 3.9 6.1 - - - -
325L NAG 4.4 6.3 - - - +
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Residues in contact with PHE 21 (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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5L TYR* 3.9 16.6 - + + -
6L ASN 3.1 15.9 - - - -
7L TYR* 3.4 43.1 - + + -
20L VAL* 1.3 75.7 - - - +
22L TYR* 1.3 83.8 + - - +
23L ASP* 3.9 13.5 - - + -
31L THR* 4.4 3.6 - - + -
32L LYS* 3.3 7.8 - - - +
33L ILE* 2.7 51.2 + - + +
64L TYR* 3.2 48.2 - + + -
66L PHE* 3.7 21.8 - + + -
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Residues in contact with TYR 22 (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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4L LYS 3.6 1.6 - - - +
5L TYR* 3.5 4.9 - - - -
6L ASN* 2.9 44.6 + - + +
20L VAL* 4.3 20.4 - - + +
21L PHE* 1.3 83.9 - - - +
23L ASP* 1.3 60.8 + - - +
24L HIS* 3.9 24.8 - + + -
29L LEU* 3.9 21.5 - - + -
31L THR 3.4 1.8 - - - -
32L LYS* 3.6 42.5 + - + -
325L NAG 3.0 34.8 + - - -
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Residues in contact with ASP 23 (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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3L LEU* 3.6 5.0 - - - +
4L LYS 3.6 2.9 - - - -
5L TYR* 3.2 18.1 - - - -
21L PHE* 3.9 8.5 - - + -
22L TYR* 1.3 72.5 - - - +
24L HIS* 1.3 60.7 + - - +
29L LEU* 3.6 4.0 - - - +
30L VAL* 2.7 42.2 + - - +
31L THR* 2.9 28.0 + - - +
64L TYR* 2.9 22.2 + - - -
170L TYR* 2.6 36.5 + - - -
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Residues in contact with HIS 24 (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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2L THR 3.7 0.5 - - - +
3L LEU* 3.4 4.2 - - - +
4L LYS* 2.8 69.3 + - + +
6L ASN* 5.9 0.4 - - + -
22L TYR* 3.9 31.3 - - + +
23L ASP* 1.3 75.9 + - - +
25L TYR* 1.3 60.1 + - - +
26L ASN 3.8 12.5 + - - +
27L ASP* 4.4 8.3 + - - -
28L GLN 3.4 3.1 + - - -
29L LEU* 3.4 40.5 + - + +
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Residues in contact with TYR 25 (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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1L ILE* 3.1 29.7 - - + +
2L THR 3.2 15.7 - - - -
3L LEU* 4.4 2.9 - - + -
24L HIS* 1.3 70.6 - - - +
26L ASN* 1.3 85.2 + - - +
28L GLN* 2.8 27.0 + - + +
30L VAL* 3.8 19.7 - - + +
50L TRP* 4.0 7.9 - + + -
167L ILE* 4.1 17.9 - - + -
170L TYR* 3.5 32.5 - + + -
171L GLN* 3.3 27.7 - - - +
174L ALA* 3.7 27.6 - - + -
178L ILE* 3.9 9.6 - - + -
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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