Contacts of the strand formed by residues 49 - 58 (chain A) in PDB entry 5Z8N
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 TYR 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37A VAL 3.8 0.2 - - - +
38A LEU* 3.1 8.0 - - - -
39A MET* 2.8 51.1 + - + +
40A ARG 4.2 2.9 - - - -
41A PRO* 3.2 37.5 - - + +
42A SER 4.9 1.8 + - - -
43A ASP* 5.8 2.8 + - - -
46A LYS* 5.0 16.8 - - + +
47A PRO 5.3 1.6 - - - -
48A PRO* 1.3 73.8 - - - +
50A VAL* 1.3 60.2 + - - +
51A ALA 4.1 0.4 - - - -
70A TRP* 3.4 31.4 - + + -
76A GLU* 4.6 16.2 - - - -
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Residues in contact with VAL 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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36A CYS* 4.8 0.2 - - + -
37A VAL 3.5 2.9 - - - +
38A LEU* 3.7 18.6 - - + -
48A PRO 4.0 5.6 - - - +
49A TYR* 1.3 79.5 - - - +
51A ALA* 1.3 63.8 + - - +
70A TRP* 3.9 3.4 - - - -
71A TYR* 3.0 51.5 + - + +
73A ARG* 6.6 0.4 - - + -
90A LEU* 3.9 18.6 - - + -
108A CYS* 3.7 24.5 - - - -
110A VAL* 4.0 5.2 - - + -
127A TYR* 3.9 26.5 - - + +
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Residues in contact with ALA 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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36A CYS* 3.3 3.3 - - - +
37A VAL* 2.8 37.8 + - - +
39A MET* 4.5 9.4 - - + +
49A TYR 4.1 0.4 - - - -
50A VAL* 1.3 74.8 - - - +
52A ARG* 1.3 60.5 + - - +
68A CYS* 4.1 21.5 - - + -
69A ARG 3.3 13.5 - - - +
70A TRP* 3.6 24.2 - - + -
71A TYR* 4.3 5.4 - - - -
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Residues in contact with ARG 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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34A GLY* 3.8 18.6 - - - +
35A ASP 3.5 10.8 - - - +
36A CYS* 4.3 4.5 - - - +
51A ALA* 1.3 72.5 - - - +
53A VAL* 1.3 73.3 + - - +
54A GLU* 2.7 30.2 + - - +
68A CYS* 3.6 2.8 - - - -
69A ARG* 2.8 70.9 + - + +
71A TYR* 4.0 30.2 + - + -
92A LEU* 4.4 15.3 - - + +
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Residues in contact with VAL 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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31A VAL* 4.0 17.5 - - + -
32A ARG 4.2 7.6 - - - +
33A ALA* 4.1 8.1 - - - -
34A GLY* 2.6 31.2 + - - -
35A ASP 2.9 15.1 + - - +
37A VAL* 3.6 27.1 - - + -
39A MET* 5.2 1.6 - - + -
52A ARG* 1.3 75.3 - - - +
54A GLU* 1.3 59.7 + - - +
55A LYS 4.0 9.9 - - - +
56A ILE* 3.9 30.7 - - + -
66A VAL* 4.7 9.6 - - + -
67A HIS 3.7 5.8 - - - +
68A CYS* 5.0 2.7 - - - +
104A ILE* 4.8 7.0 - - + -
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Residues in contact with GLU 54 (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 ALA* 3.5 17.1 - - - +
34A GLY 4.6 0.2 - - - +
52A ARG* 2.7 53.8 + - - +
53A VAL* 1.3 76.3 - - - +
55A LYS* 1.3 65.8 + - + +
67A HIS* 2.9 16.3 + - + +
68A CYS 4.5 1.6 - - - -
69A ARG* 3.9 18.5 + - + +
96A PHE* 3.5 20.0 - - + -
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Residues in contact with LYS 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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18A GLU* 3.1 42.6 + - + +
33A ALA* 4.6 3.4 - - - -
53A VAL* 3.8 1.8 - - - +
54A GLU* 1.3 82.4 - - + +
56A ILE* 1.3 69.2 + - - +
57A GLU* 3.8 22.7 - - + -
66A VAL* 3.4 5.7 - - - +
67A HIS* 2.8 60.2 + - + +
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Residues in contact with ILE 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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18A GLU* 3.4 7.5 - - - +
19A LEU* 2.5 60.4 + - + +
20A ASP 4.3 5.4 - - - +
21A SER 4.2 2.7 - - - +
22A TYR* 3.9 27.8 - - + +
31A VAL* 3.3 34.1 - - + +
32A ARG* 4.2 7.9 - - - -
33A ALA* 4.5 4.8 - - + +
53A VAL* 3.9 17.9 - - + -
55A LYS* 1.3 76.1 - - - +
57A GLU* 1.3 61.9 + - - +
64A VAL* 5.1 2.7 - - + -
65A LYS 3.8 8.3 - - - +
66A VAL* 4.4 10.5 - - + -
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Residues in contact with GLU 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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16A ARG* 2.5 51.5 + - + +
17A LYS 3.0 17.0 - - - +
18A GLU* 4.0 5.2 - - + +
19A LEU* 3.9 6.3 - - - +
55A LYS* 3.8 17.9 - - - -
56A ILE* 1.3 77.3 - - - +
58A ALA* 1.3 57.4 + - - +
59A ASP 4.0 0.2 + - - -
64A VAL* 4.6 1.1 - - - -
65A LYS* 2.8 40.8 + - + +
67A HIS* 2.9 32.2 + - + +
98A VAL* 5.3 0.2 - - - +
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Residues in contact with ALA 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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16A ARG* 3.4 10.5 - - - +
17A LYS* 2.9 32.5 + - + +
19A LEU* 3.4 28.2 - - + +
57A GLU* 1.3 72.3 - - - +
59A ASP* 1.3 68.7 + - - +
62A ASN* 4.5 23.1 - - - +
63A ASN 4.0 4.0 - - - -
64A VAL* 4.2 8.5 - - + +
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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