Contacts of the strand formed by residues 19 - 26 (chain A) in PDB entry 5T4S
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 GLN 19 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A THR 3.4 1.7 - - - +
14A ASN* 3.7 1.2 - - - -
15A TYR* 2.7 64.8 + - + +
18A THR* 1.3 88.9 + - - +
20A TYR* 1.3 62.7 + - - +
21A TYR* 4.1 5.6 - - + -
121A LEU 2.9 25.3 + - - -
123A GLU* 2.7 29.2 + - - +
124A PHE* 3.2 31.6 - - + -
230A SER* 5.2 0.4 - - - +
402A PG6 3.8 16.2 - - - -
403A DMS 3.5 8.1 - - + +
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 4.4 8.1 - - + +
13A THR 3.3 6.1 - - - +
14A ASN* 3.0 35.2 + - + -
17A ASP* 3.4 16.1 + - - -
19A GLN* 1.3 75.5 - - - +
21A TYR* 1.3 60.6 + - - +
36A VAL* 3.6 15.1 - - - +
37A PHE 4.5 2.1 + - - -
162A TYR* 3.5 56.3 + + + -
163A ASN 2.7 20.8 + - - -
173A GLY 3.3 21.8 - - - -
174A GLY* 4.9 1.3 - - - -
317A ALA* 3.7 24.2 - - + -
321A ARG* 3.1 21.2 + - - -
403A DMS 2.7 21.8 + - + +
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Residues in contact with TYR 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU* 3.2 10.0 - - - +
13A THR* 2.8 72.5 + - + +
15A TYR* 4.0 14.8 - - + +
19A GLN* 4.2 10.1 - - + -
20A TYR* 1.3 75.5 - - - +
22A GLY* 1.3 60.4 + - - +
23A GLU* 5.4 1.6 - - - -
34A LYS* 3.7 38.2 + - + +
35A VAL 3.2 20.9 - - - +
36A VAL* 4.4 1.1 - - + +
123A GLU* 3.5 43.9 + - + -
124A PHE* 4.0 15.0 - - + -
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Residues in contact with GLY 22 (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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10A VAL* 4.3 2.0 - - - -
11A ILE 3.6 15.7 - - - -
12A LEU* 3.5 11.2 - - - +
21A TYR* 1.3 76.2 - - - +
23A GLU* 1.3 63.6 + - - -
33A PHE 3.4 1.0 - - - +
34A LYS* 3.3 4.6 - - - -
35A VAL* 2.8 38.2 + - - +
37A PHE* 4.1 6.0 - - - -
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Residues in contact with GLU 23 (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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10A VAL* 4.3 12.7 - - - +
11A ILE 4.5 3.2 + - - -
21A TYR* 5.4 1.6 - - - -
22A GLY* 1.3 72.7 - - - +
24A ILE* 1.3 66.8 + - - +
32A THR* 4.3 24.7 - - + -
33A PHE 3.4 6.7 - - - +
34A LYS* 3.5 27.9 + - - +
98A THR 4.6 1.0 - - - +
99A VAL* 4.9 4.3 - - - -
100A GLY 5.2 1.4 + - - -
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Residues in contact with ILE 24 (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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22A GLY 4.0 0.2 + - - -
23A GLU* 1.3 79.1 - - - +
25A GLY* 1.3 58.4 + - - +
26A ILE* 3.9 29.2 - - + -
31A GLN 3.9 0.3 - - - +
32A THR* 3.2 7.3 - - - -
33A PHE* 2.9 40.9 + - + +
35A VAL* 3.7 39.3 - - + -
37A PHE* 3.8 14.8 - - + -
44A VAL* 4.7 5.8 - - + -
46A VAL* 4.7 2.0 - - + -
97A ILE* 4.1 12.1 - - + -
98A THR 3.3 15.7 - - - +
99A VAL* 3.9 13.2 - - + -
128A VAL* 4.1 14.8 - - + -
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Residues in contact with GLY 25 (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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24A ILE* 1.3 72.8 - - - +
26A ILE* 1.3 62.1 + - - -
27A GLY 4.2 0.2 - - - -
30A PRO* 4.3 13.0 - - - -
31A GLN 3.4 8.7 - - - -
32A THR* 4.3 4.3 - - - -
96A ILE* 3.7 1.7 - - - +
97A ILE* 3.2 5.8 - - - +
98A THR* 2.8 49.2 + - - -
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Residues in contact with ILE 26 (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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24A ILE* 3.9 15.7 - - + -
25A GLY* 1.3 75.3 - - - -
27A GLY* 1.3 62.9 + - - +
31A GLN* 2.7 46.4 + - - +
33A PHE* 3.6 22.9 - - + -
44A VAL* 5.4 0.7 - - + -
46A VAL* 3.6 30.5 - - + -
64A PHE* 3.5 24.7 - - + -
95A ASP* 3.9 6.5 - - + -
96A ILE 3.4 4.0 - - - +
97A ILE* 3.8 21.1 - - + -
108A PHE* 3.6 28.3 - - + -
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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