Contacts of the strand formed by residues 54 - 61 (chain A) in PDB entry 5NUJ
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 LEU 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ILE* 4.1 22.4 - - + -
15A VAL* 4.5 4.3 - - + -
46A LEU* 4.5 24.7 - - + -
47A LYS 3.8 15.3 - - - +
48A PRO* 4.1 13.5 - - + -
53A ASP* 1.3 74.6 - - - +
55A GLU* 1.3 64.0 + - - +
56A PHE* 4.3 25.8 + - + -
71A ILE 4.1 0.2 - - - +
72A ILE* 3.5 2.1 - - - -
73A ALA* 2.6 48.3 + - + +
82A PHE* 4.1 29.1 - - + -
92A VAL* 5.3 1.8 - - + -
94A VAL* 5.2 7.4 - - + -
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Residues in contact with GLU 55 (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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45A GLU 3.8 0.3 - - - +
46A LEU* 3.7 4.4 - - - +
47A LYS* 2.6 86.9 + - + +
49A THR* 4.9 7.2 - - + +
54A LEU* 1.3 76.5 - - - +
56A PHE* 1.3 66.1 + - - +
70A LYS* 3.1 31.8 - - + +
71A ILE 3.4 10.8 - - - +
72A ILE* 3.0 33.6 - - + +
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Residues in contact with PHE 56 (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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43A VAL* 4.7 1.6 - - + -
45A GLU 3.8 2.5 - - - -
46A LEU* 3.7 24.9 - - + -
54A LEU* 4.4 22.0 - - + -
55A GLU* 1.3 78.3 - - - +
57A LEU* 1.3 61.2 + - - +
58A LEU* 3.9 17.0 - - + -
70A LYS* 3.4 13.2 - - - +
71A ILE* 2.7 55.9 + - + -
73A ALA* 4.3 21.3 - - + -
84A ILE* 5.6 0.2 - - + -
92A VAL* 4.2 26.9 - - + -
105A PHE* 4.4 20.9 - + - -
201A Z80 3.4 25.6 - + + -
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Residues in contact with LEU 57 (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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43A VAL* 3.7 0.3 - - - -
44A GLU* 2.9 37.0 + - + -
45A GLU* 2.9 49.1 + - + +
47A LYS* 4.1 11.9 - - + -
56A PHE* 1.3 71.6 - - - +
58A LEU* 1.3 69.3 + - - +
68A GLN* 3.5 27.4 - - - +
69A LYS 3.6 8.5 - - - +
70A LYS* 3.7 36.1 - - + +
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Residues in contact with LEU 58 (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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41A VAL* 4.5 17.5 - - + -
42A TYR 3.0 13.9 - - - +
43A VAL* 3.4 31.2 - - + -
44A GLU* 4.4 2.9 - - - +
56A PHE* 3.9 17.9 - - + +
57A LEU* 1.3 85.2 - - - +
59A GLN* 1.3 69.3 + - - +
68A GLN* 3.6 8.5 + - - +
69A LYS* 3.0 39.8 + - + +
71A ILE* 4.0 11.9 - - + +
201A Z80 3.3 43.1 - - + -
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Residues in contact with GLN 59 (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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41A VAL* 3.7 4.9 - - - +
42A TYR* 2.8 44.8 + - + +
44A GLU* 3.0 41.4 + - + +
58A LEU* 1.3 78.6 - - - +
60A LYS* 1.3 61.7 + - - +
66A CYS* 3.4 9.2 - - - -
67A ALA 3.3 13.0 - - - +
68A GLN* 5.0 8.0 - - + +
69A LYS* 6.2 0.4 - - - -
158A GLU 4.3 2.0 + - - +
159A GLN* 3.3 27.4 + - - +
160A CYS* 2.6 34.2 + - - -
161A HIS* 5.7 0.2 - - - -
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Residues in contact with LYS 60 (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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35A GLN 4.2 0.6 + - - -
36A SER* 2.5 36.4 + - - +
37A ALA 3.0 18.2 + - - -
38A PRO* 4.0 14.1 - - - -
40A ARG 3.3 19.3 + - - +
41A VAL* 3.8 13.5 - - + -
42A TYR* 4.9 0.4 - - - -
59A GLN* 1.3 73.6 - - - +
61A TRP* 1.3 72.8 + - - +
62A GLU* 3.6 8.1 + - + +
67A ALA* 2.7 39.1 + - - +
68A GLN* 5.4 0.4 - - - +
69A LYS* 3.8 27.8 - - + +
160A CYS* 3.8 5.4 - - - -
201A Z80 4.6 11.9 - - - -
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Residues in contact with TRP 61 (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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35A GLN* 3.5 48.3 + - + +
36A SER* 4.0 19.4 - - - -
40A ARG 5.2 0.2 + - - -
42A TYR* 5.1 0.6 - - - -
60A LYS* 1.3 94.6 + - - +
62A GLU* 1.3 61.8 + - - +
63A ASN 4.4 9.4 + - - -
64A GLY* 3.7 18.1 - - - -
65A GLU* 3.5 19.3 - - + +
66A CYS* 3.4 35.7 - - + -
159A GLN 5.4 0.9 - - - -
160A CYS* 3.8 17.9 - - + -
162A ILE* 4.8 10.1 - - - -
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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