Contacts of the strand formed by residues 53 - 60 (chain I) in PDB entry 5A2Q
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 LYS 53 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3082 G 2.8 46.1 + - - -
3092 G 4.1 7.9 + - - +
45I THR* 4.6 9.6 - - - -
46I VAL 3.6 8.1 - - - +
47I ARG* 5.7 3.8 - - + -
48I VAL* 5.2 0.2 - - - -
51I GLY 5.2 2.5 - - - +
52I ASN* 1.3 76.1 - - - +
54I LYS* 1.3 61.1 + - - +
55I TYR* 3.7 43.1 + - + +
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Residues in contact with LYS 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3802 G 3.5 21.2 + - - +
3812 C 2.9 28.2 + - - +
3822 C 2.9 33.1 + - - -
45I THR* 3.6 2.1 - - - -
46I VAL* 2.8 48.8 + - + +
48I VAL* 3.7 24.7 - - + -
52I ASN 3.6 2.2 + - - -
53I LYS* 1.3 72.9 - - - +
55I TYR* 1.3 61.5 + - - +
56I ARG* 3.7 6.2 + - + +
181I GLN* 3.7 39.9 - - + +
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Residues in contact with TYR 55 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3052 U 3.1 63.9 - + - +
3082 G 4.9 0.7 - - - -
3092 G 2.1 42.0 + - - -
43I ILE* 5.0 2.7 - - + -
44I HIS 4.4 0.4 - - - -
45I THR* 3.4 33.4 - - + -
53I LYS* 3.7 29.0 + - + +
54I LYS* 1.3 71.8 - - - +
56I ARG* 1.3 60.1 + - - +
180I GLY 3.5 1.2 - - - +
181I GLN 3.1 22.5 + - - +
182I CYS 3.3 13.9 - - - +
183I GLY* 3.2 13.8 + - - -
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Residues in contact with ARG 56 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3792 C 3.7 17.8 + - - -
3802 G 2.6 44.0 + - - -
17402 C 6.1 0.9 - - - -
31I ARG* 4.3 14.1 - - - +
32I PRO* 4.3 10.0 + - - +
34I ALA* 3.4 26.5 - - + +
43I ILE* 3.2 10.6 - - - +
44I HIS* 2.9 48.2 + - + +
46I VAL* 4.1 25.5 - - + +
54I LYS* 3.7 5.7 + - + +
55I TYR* 1.3 74.3 - - - +
57I ALA* 1.3 63.9 + - - +
58I LEU* 3.9 11.2 + - + -
180I GLY 3.0 18.8 + - - +
181I GLN* 4.0 4.9 - - - +
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Residues in contact with ALA 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I ALA* 4.8 2.9 - - - +
35I ASN 3.8 0.3 - - - +
36I THR* 2.6 36.0 + - + +
42I ARG 3.8 3.1 - - - -
43I ILE* 4.1 9.4 - - + -
56I ARG* 1.3 76.2 - - - +
58I LEU* 1.3 66.6 + - - +
60I LEU* 4.2 14.8 - - + -
179I PRO* 3.6 35.5 + - + +
180I GLY* 4.1 0.8 + - - -
183I GLY* 4.5 6.3 - - - +
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Residues in contact with LEU 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17402 C 3.6 23.8 - - - +
17412 U 3.5 22.9 - - - +
34I ALA* 4.5 16.8 - - + -
35I ASN* 3.8 15.1 - - - +
36I THR* 3.7 2.1 - - - -
37I LYS* 3.0 27.0 + - - +
42I ARG* 3.0 16.8 + - + +
44I HIS* 3.4 43.1 - - + +
56I ARG* 3.9 9.4 + - + +
57I ALA* 1.3 81.3 - - - +
59I ARG* 1.3 65.5 + - + +
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Residues in contact with ARG 59 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17412 U 3.6 20.5 + - - -
17422 C 3.2 25.4 + - - -
36I THR* 4.7 0.2 - - - -
37I LYS* 3.2 22.8 - - + +
38I ILE 6.3 0.4 - - - -
39I GLY* 4.3 7.2 - - - +
40I PRO* 3.2 40.4 - - - +
41I ARG* 3.4 1.5 - - - -
42I ARG* 2.9 66.9 + - + +
58I LEU* 1.3 83.7 - - + +
60I LEU* 1.3 74.7 + - - +
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Residues in contact with LEU 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I THR* 4.3 4.0 - - + +
37I LYS 2.8 6.9 + - - -
38I ILE* 3.2 10.8 - - - +
39I GLY 2.8 26.9 + - - -
41I ARG* 4.6 18.4 - - + +
43I ILE* 4.8 3.4 - - + -
57I ALA* 4.2 13.7 - - + -
59I ARG* 1.3 82.6 - - - +
61I ASP* 1.3 62.4 + - - +
62I VAL* 4.4 12.6 - - + +
78I ILE* 5.4 1.8 - - + -
96I LEU* 4.0 17.0 - - + -
179I PRO* 4.2 11.2 - - + -
183I GLY 4.5 9.9 - - - +
184I ARG* 4.0 7.2 - - - -
185I ALA* 3.4 41.7 - - + +
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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