Contacts of the strand formed by residues 18 - 25 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8K THR 4.3 0.7 - - - -
9K VAL* 2.9 8.1 - - - +
10K THR* 2.8 38.5 + - - +
12K LYS* 3.0 41.1 - - + +
16K LEU* 4.0 1.9 + - - -
17K TYR* 1.3 75.3 - - - +
19K GLY* 1.3 59.8 + - - +
20K VAL* 6.2 1.8 - - + -
35K TYR 4.7 3.3 - - - +
37K HIS* 3.0 26.5 + - - -
70K TYR* 3.9 1.6 - - - -
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Residues in contact with GLY 19 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8K THR 3.2 6.7 - - - -
9K VAL* 4.2 0.7 - - - -
18K ASP* 1.3 78.2 + - - +
20K VAL* 1.3 65.4 + - - +
34K SER* 3.2 5.5 - - - -
35K TYR* 2.9 28.9 + - - +
66K PHE* 3.9 7.4 - - - -
70K TYR* 3.7 25.1 - - - -
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Residues in contact with VAL 20 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K ASN 3.7 1.0 - - - +
7K TYR* 3.5 2.1 - - - -
8K THR* 2.8 52.9 + - + +
10K THR* 5.7 2.2 - - - +
18K ASP* 5.9 2.5 - - + -
19K GLY* 1.3 79.7 - - - +
21K PHE* 1.3 62.2 + - - +
22K TYR* 4.3 16.4 - - + +
32K LYS* 4.6 14.1 - - - -
33K ILE 3.1 11.0 - - - +
34K SER* 4.0 11.0 - - - -
66K PHE* 3.9 5.5 - - - -
325K NAG 4.2 17.5 - - - -
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Residues in contact with PHE 21 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5K TYR* 3.9 16.6 - + + -
6K ASN 3.1 12.8 - - - -
7K TYR* 3.4 47.8 - + + -
20K VAL* 1.3 76.6 - - - +
22K TYR* 1.3 82.6 + - - +
23K ASP* 3.9 13.9 - - + -
31K THR* 4.3 3.8 - - + -
32K LYS* 3.3 8.0 - - - +
33K ILE* 2.7 51.7 + - + +
64K TYR* 3.2 46.0 - + + -
66K PHE* 3.7 21.8 - + + -
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Residues in contact with TYR 22 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4K LYS 3.6 1.6 - - - +
5K TYR* 3.5 4.9 - - - -
6K ASN* 2.9 43.7 + - + +
8K THR* 6.0 0.2 - - - -
20K VAL* 4.3 18.4 - - + +
21K PHE* 1.3 86.2 - - - +
23K ASP* 1.3 60.5 + - - +
24K HIS* 3.9 23.5 - - + -
29K LEU* 3.9 22.2 - - + -
31K THR 3.4 2.2 - - - -
32K LYS* 3.7 42.3 + - + -
325K NAG 3.0 38.8 + - - -
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Residues in contact with ASP 23 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3K LEU* 3.6 4.7 - - - +
4K LYS 3.6 2.9 - - - -
5K TYR* 3.2 17.8 - - - -
21K PHE* 3.9 8.3 - - + -
22K TYR* 1.3 73.2 - - - +
24K HIS* 1.3 58.5 + - - +
29K LEU* 3.6 4.0 - - - +
30K VAL* 2.7 41.8 + - - +
31K THR* 2.9 27.5 + - - +
64K TYR* 2.8 23.2 + - - -
170K TYR* 2.6 36.5 + - - -
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Residues in contact with HIS 24 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2K THR* 3.7 0.7 - - - +
3K LEU* 3.4 3.6 - - - +
4K LYS* 2.8 68.8 + - + +
6K ASN* 5.9 0.9 - - + -
22K TYR* 3.9 31.7 - + + +
23K ASP* 1.3 76.0 + - - +
25K TYR* 1.3 60.9 + - - +
26K ASN 3.8 12.2 + - - +
27K ASP* 4.4 8.0 + - - -
28K GLN 3.4 3.3 + - - -
29K LEU* 3.4 39.7 + - + +
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Residues in contact with TYR 25 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1K ILE* 3.2 29.3 - - + +
2K THR 3.3 16.8 - - - -
3K LEU* 4.4 2.9 - - + -
24K HIS* 1.3 71.0 - - - +
26K ASN* 1.3 84.8 + - - +
28K GLN* 2.8 28.1 + - + +
30K VAL* 3.8 19.8 - - + +
50K TRP* 4.1 7.2 - + + -
167K ILE* 4.0 17.5 - - + -
170K TYR* 3.5 33.9 - + + -
171K GLN* 3.3 28.6 - - - +
174K ALA* 3.7 27.8 - - + -
178K ILE* 3.9 9.4 - - + -
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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