Contacts of the strand formed by residues 46 - 53 (chain A) in PDB entry 1X49
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 ARG 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A THR* 3.2 4.5 - - - +
39A SER* 3.0 43.3 + - - +
40A GLY* 5.4 1.8 - - - -
41A PRO* 5.7 0.7 - - + -
44A ASP* 3.1 32.0 + - - +
45A ARG* 1.3 73.0 - - - +
47A PHE* 1.3 62.8 + - - +
48A THR* 3.7 3.5 + - - -
62A LYS* 4.5 22.7 - - + +
63A GLY* 3.9 8.4 - - - +
64A ARG* 3.7 46.1 - - - +
68A GLU* 4.3 7.1 + - - -
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Residues in contact with PHE 47 (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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36A LEU 5.5 1.8 - - - +
37A SER 4.4 3.8 - - - +
38A THR* 3.2 31.2 - - + -
45A ARG* 4.4 15.0 - - + -
46A ARG* 1.3 71.4 - - - +
48A THR* 1.3 60.3 + - - +
49A PHE* 4.2 7.2 - - + -
62A LYS* 4.6 0.2 - - - -
63A GLY 3.1 17.4 + - - +
64A ARG 3.2 28.3 - - - -
65A SER* 3.6 9.4 - - - -
66A LYS* 3.4 56.8 - - + +
69A ALA* 2.9 24.8 - - + +
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Residues in contact with THR 48 (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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36A LEU* 3.1 48.3 + - + +
37A SER 3.4 17.9 + - - -
39A SER* 4.6 10.6 + - - -
46A ARG 4.2 4.5 + - - -
47A PHE* 1.3 72.8 - - - +
49A PHE* 1.3 73.7 + - - +
60A GLU* 3.2 28.6 + - + +
61A ALA 3.2 16.2 - - - +
62A LYS* 4.0 16.9 - - + +
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Residues in contact with PHE 49 (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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33A TYR* 5.0 4.0 - - + -
34A LYS 3.4 15.3 - - - -
35A GLU* 3.4 36.1 - - + -
36A LEU* 3.7 7.0 - - - -
47A PHE* 4.2 4.9 - - + -
48A THR* 1.3 89.7 - - - +
50A GLN* 1.3 60.1 + - - +
60A GLU* 2.9 1.7 - - - -
61A ALA 2.7 37.0 + - - -
66A LYS* 3.7 42.2 - - + -
69A ALA* 3.4 20.2 - - + +
70A ARG* 3.3 64.8 - - + +
73A ALA* 3.1 6.7 - - + +
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Residues in contact with GLN 50 (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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33A TYR* 3.3 6.6 - - - +
34A LYS* 2.9 52.4 + - + +
36A LEU* 3.2 24.1 - - + +
49A PHE* 1.3 78.3 - - - +
51A VAL* 1.3 64.1 + - - +
52A LEU* 4.0 12.2 - - + +
57A GLU* 4.3 25.1 + - - +
58A PHE 3.0 32.6 + - - +
59A PRO 4.7 0.4 - - - -
60A GLU* 3.4 24.2 + - + +
73A ALA* 3.8 7.0 - - - -
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Residues in contact with VAL 51 (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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20A LEU* 4.1 12.6 - - + -
31A ILE* 3.0 33.7 - - + -
32A THR 3.2 5.8 - - - +
33A TYR* 3.4 33.9 - - + -
50A GLN* 1.3 75.7 - - - +
52A LEU* 1.3 75.1 + - - +
53A ILE* 4.0 14.8 - - + -
58A PHE* 3.2 34.5 + - + +
73A ALA* 4.5 5.2 - - + +
74A ALA* 4.4 15.5 - - - +
77A ALA* 4.7 9.6 - - + -
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Residues in contact with LEU 52 (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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30A ALA 2.7 22.0 - - - +
31A ILE* 3.2 0.7 - - - -
32A THR* 2.7 50.3 + - + +
34A LYS* 4.0 22.4 - - + +
50A GLN* 4.0 20.4 - - + -
51A VAL* 1.3 81.2 - - - +
53A ILE* 1.3 55.6 + - - +
55A GLU* 4.9 7.8 + - - +
56A LYS 3.0 22.2 - - - +
57A GLU* 4.0 22.4 - - + +
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Residues in contact with ILE 53 (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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20A LEU* 3.5 29.6 - - + -
23A TYR* 4.6 6.7 - - + -
29A VAL* 3.4 35.7 - - + -
30A ALA 3.3 2.2 - - - +
31A ILE* 3.9 19.3 - - + -
51A VAL* 4.0 4.9 - - + -
52A LEU* 1.3 75.9 - - - +
54A ASP* 1.3 68.4 + - + +
55A GLU 3.3 1.1 - - - -
56A LYS* 2.8 33.9 + - - +
58A PHE* 3.5 33.9 - - + -
77A ALA* 4.4 2.2 - - + -
81A LEU* 4.0 14.4 - - + -
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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