Contacts of the strand formed by residues 2 - 12 (chain A) in PDB entry 5T5I
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 GLU 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 84.2 - - - +
3A TYR* 1.3 64.9 + - - +
26A VAL 3.3 4.5 - - - +
27A LYS* 4.0 32.8 + - + +
35A VAL* 3.5 17.9 - - + +
36A SER* 2.7 48.2 + - - -
38A SER* 4.0 7.1 + - - -
39A ALA* 3.7 16.0 + - + -
40A LYS* 3.0 22.8 + - - +
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Residues in contact with TYR 3 (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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1A MET* 3.8 17.1 - - + +
2A GLU* 1.3 74.0 - - - +
4A ILE* 1.3 59.3 + - - +
5A ILE* 4.3 1.8 - - + -
24A ILE 4.2 0.2 - - - +
25A CYS* 3.7 2.1 - - - -
26A VAL* 2.8 48.6 + - + +
35A VAL* 4.1 3.5 - - - +
39A ALA* 4.5 3.1 - - - -
40A LYS* 3.4 54.1 + - + +
42A ILE* 3.6 22.7 - - + -
497A LEU* 4.1 12.3 - - + -
500A GLY 3.4 28.9 - - - -
501A GLU* 4.5 10.1 + - - -
502A ILE* 3.5 37.6 + - + +
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Residues in contact with ILE 4 (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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3A TYR* 1.3 73.9 - - - +
5A ILE* 1.3 63.2 + - - +
6A LYS* 3.5 29.0 + - + +
23A ASP* 4.0 16.4 - - + +
24A ILE 3.5 8.5 - - - +
25A CYS* 4.1 21.1 - - - +
35A VAL* 4.2 12.8 - - + -
39A ALA* 4.4 10.1 - - + +
40A LYS 2.9 17.0 + - - +
41A VAL* 3.5 21.2 - - + -
42A ILE* 2.9 25.4 + - - -
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Residues in contact with ILE 5 (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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3A TYR* 5.4 0.9 - - + -
4A ILE* 1.3 71.5 - - - +
6A LYS* 1.3 60.2 + - - +
8A GLY 5.1 0.3 + - - -
22A MET 4.3 1.6 - - - +
23A ASP* 3.4 6.4 - - - -
24A ILE* 2.9 44.3 + - + +
26A VAL* 4.5 6.5 - - + -
42A ILE* 3.4 28.7 - - + +
44A ALA* 3.8 23.8 - - + -
49A VAL* 4.2 18.4 - - + -
467A ILE* 3.4 42.2 - - + -
469A VAL* 4.4 10.3 - - + -
497A LEU* 4.2 12.6 - - + -
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Residues in contact with LYS 6 (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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4A ILE* 3.7 27.3 - - + +
5A ILE* 1.3 71.7 - - - +
7A ASN* 1.3 83.4 + - - +
8A GLY 3.2 4.0 + - - -
23A ASP* 3.0 29.2 + - - +
41A VAL* 3.7 28.7 - - + -
42A ILE 2.8 13.2 + - - +
43A ASP* 4.1 6.4 - - - +
44A ALA* 2.8 28.9 + - - -
45A SER 3.6 0.2 + - - -
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Residues in contact with ASN 7 (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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5A ILE 4.1 0.8 + - - -
6A LYS* 1.3 92.9 - - - +
8A GLY* 1.3 62.4 + - - +
9A PHE* 4.1 2.6 + - - -
21A LYS* 3.7 42.5 - - - +
22A MET 4.3 2.6 + - - +
23A ASP* 3.1 18.0 + - - -
43A ASP* 4.3 5.9 - - - +
44A ALA 3.7 1.7 - - - +
45A SER* 3.6 28.4 + - - -
46A GLY 4.3 2.6 + - - -
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Residues in contact with GLY 8 (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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5A ILE 5.1 0.6 + - - -
6A LYS 3.2 4.9 + - - -
7A ASN* 1.3 79.3 - - - +
9A PHE* 1.3 61.0 - - - -
10A VAL* 3.4 4.2 + - - -
21A LYS* 3.3 3.1 - - - -
22A MET 3.2 31.8 + - - +
44A ALA* 3.2 26.8 - - - +
47A LYS 3.7 2.5 - - - -
49A VAL* 3.9 10.5 - - - +
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Residues in contact with PHE 9 (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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7A ASN 5.3 1.8 - - - -
8A GLY* 1.3 68.4 - - - -
10A VAL* 1.3 62.4 + - - +
11A TYR* 3.5 13.0 - - + -
19A GLY* 3.6 20.2 - - - +
20A GLU 3.6 3.6 - - - -
21A LYS* 4.4 25.1 - - + -
46A GLY* 4.1 17.7 - - - -
47A LYS 2.9 22.1 + - - +
48A ILE* 3.6 0.9 - - - -
49A VAL 3.1 19.8 + - - -
473A ASN* 3.7 19.1 - - - -
474A PRO* 3.6 33.4 - - + -
475A GLU* 3.5 40.6 - - + -
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Residues in contact with VAL 10 (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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8A GLY 3.9 4.3 - - - +
9A PHE* 1.3 73.2 - - - +
11A TYR* 1.4 60.0 - - - +
12A CYS* 4.1 5.8 - - + +
17A VAL* 3.5 22.1 - - + +
19A GLY* 2.8 28.8 + - - -
20A GLU 2.8 20.5 + - - +
22A MET* 3.6 35.0 - - + +
24A ILE* 4.1 22.9 - - + -
49A VAL* 3.5 13.9 - - + -
459A LEU* 3.7 23.8 - - + -
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Residues in contact with TYR 11 (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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9A PHE* 3.5 22.0 - - + -
10A VAL* 1.4 71.0 - - - +
12A CYS* 1.4 58.9 + - - +
13A PRO* 3.8 5.5 - - + +
17A VAL 3.5 2.7 - - - +
18A ASP* 3.5 24.2 - - - -
19A GLY* 3.4 26.6 - - - -
48A ILE* 3.9 31.2 - - + -
49A VAL 3.0 11.2 + - - +
50A MET* 3.8 16.6 - - + +
51A PRO* 3.4 23.6 - - - +
435A PHE* 3.6 26.5 - - + -
436A SER* 3.8 17.7 - - - -
439A ALA* 4.4 10.2 - - + +
459A LEU* 4.2 0.7 - - - +
474A PRO* 3.5 23.6 - - + +
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Residues in contact with CYS 12 (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* 4.1 4.7 - - + -
11A TYR* 1.4 72.8 - - - +
13A PRO* 1.4 68.4 - - - +
14A LEU 4.3 1.8 - - - -
15A ASN* 3.1 38.2 + - + -
16A GLY 3.1 4.3 + - - -
17A VAL* 2.9 41.9 + - + +
51A PRO* 4.8 2.9 - - - -
457A GLY 4.9 0.2 - - - -
458A HIS* 3.6 12.3 - - - -
459A LEU* 3.2 34.8 - - + +
460A GLY 4.6 0.2 - - - -
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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