Contacts of the strand formed by residues 43 - 51 (chain G) in PDB entry 4Z94
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 ALA 43 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21G ARG* 3.8 2.4 - - - +
22G VAL* 3.1 27.9 + - + +
42G ASP* 1.3 77.3 - - - +
44G TYR* 1.3 69.6 + - - +
64G TRP 3.2 11.2 - - - +
65G LEU* 4.1 7.2 - - + -
69G CYS* 4.2 4.7 - - - -
73G GLU* 3.8 35.6 + - + +
74G SER* 4.0 10.1 - - - +
77G ALA* 4.1 4.0 - - + -
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Residues in contact with TYR 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19G ILE* 3.9 7.2 - - + -
20G TRP 3.4 17.5 - - - +
21G ARG* 3.5 30.7 - - + -
30G VAL* 3.8 13.7 - - + -
37G ASP 4.1 6.7 + - - -
38G PHE* 3.4 46.3 - + + -
39G PHE* 3.2 38.6 + - - +
42G ASP* 3.8 20.0 - - + -
43G ALA* 1.3 79.5 - - - +
45G VAL* 1.3 63.5 + - - +
46G ILE* 3.9 8.7 - - + -
63G TYR* 3.2 6.1 - - - +
64G TRP* 2.5 51.4 + + + +
77G ALA* 4.2 2.5 - - - +
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Residues in contact with VAL 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ILE* 3.6 0.7 - - - -
20G TRP* 2.9 43.7 + - + +
21G ARG* 5.1 0.2 - - - +
22G VAL* 4.6 2.2 - - + -
27G LEU* 3.7 28.7 - - + -
44G TYR* 1.3 75.0 - - - +
46G ILE* 1.3 62.8 + - - +
61G LEU* 4.1 14.8 - - + -
62G HIS 3.5 4.9 - - - +
63G TYR* 4.4 0.2 - - - +
77G ALA* 4.0 28.0 - - + +
80G PHE* 4.3 3.6 - - + -
81G THR* 4.2 14.8 - - - +
84G LEU* 4.1 25.8 - - + -
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Residues in contact with ILE 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17G LEU* 3.6 27.4 - - + -
18G GLN 3.4 6.5 - - - +
19G ILE* 4.0 25.4 - - + -
38G PHE* 4.0 3.8 - - + -
44G TYR* 3.9 12.8 - - + -
45G VAL* 1.3 77.9 - - - +
47G LEU* 1.3 62.5 + - - +
60G ASP 3.8 1.4 - - - +
61G LEU* 3.5 6.9 - - - +
62G HIS* 2.7 45.7 + - + +
64G TRP* 3.8 19.3 - - + +
106G PHE* 3.5 42.2 - - + -
109G TYR* 4.4 9.9 - - + -
110G PHE* 5.3 0.7 - - + -
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Residues in contact with LEU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ALA* 4.1 12.8 - - + -
12G GLY* 3.5 21.5 - - - +
16G GLY 3.7 1.2 - - - +
17G LEU* 3.5 8.4 - - - -
18G GLN* 2.8 54.7 + - + +
20G TRP* 3.8 18.1 - - + -
45G VAL 4.3 0.2 - - - -
46G ILE* 1.3 71.2 - - - +
48G LYS* 1.3 62.7 + - - +
49G THR* 3.8 8.5 + - - +
59G TYR* 3.7 30.5 - - + -
60G ASP 3.6 9.9 - - - +
61G LEU* 4.1 20.9 - - + -
84G LEU* 5.2 1.8 - - + -
88G LEU* 4.5 7.6 - - + -
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Residues in contact with LYS 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16G GLY* 3.4 19.3 - - - +
17G LEU* 3.9 14.3 - - + +
46G ILE* 4.2 1.6 + - - +
47G LEU* 1.3 72.5 - - - +
49G THR* 1.3 68.1 + - - +
50G VAL* 4.0 19.4 + - + +
58G GLN 3.6 1.9 - - - +
59G TYR* 3.6 2.4 - - - -
60G ASP* 2.8 43.1 + - + +
109G TYR* 3.6 52.2 - - + +
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Residues in contact with THR 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G GLY* 3.7 17.7 - - - -
14G GLU 3.5 33.5 + - - +
15G PRO* 3.2 6.2 - - + +
16G GLY 3.0 30.9 + - - +
18G GLN* 4.4 2.6 + - - -
47G LEU* 3.8 8.9 + - - +
48G LYS* 1.3 77.8 - - - +
50G VAL* 1.3 64.5 + - - +
57G LEU* 3.9 20.6 - - + -
58G GLN 3.5 2.9 - - - -
59G TYR* 3.7 26.0 - - + -
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Residues in contact with VAL 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G PRO* 4.6 2.2 - - - -
48G LYS* 4.3 25.8 - - + +
49G THR* 1.3 76.8 - - - +
51G GLN* 1.3 73.9 + - - +
52G LEU* 5.2 1.8 - - + -
57G LEU* 3.3 10.1 - - - +
58G GLN* 2.8 67.0 + - + +
60G ASP* 5.6 0.9 - - - +
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Residues in contact with GLN 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G PRO* 3.3 26.7 - - + +
50G VAL* 1.3 86.4 - - - +
52G LEU* 1.3 73.3 + - - +
55G GLY* 3.4 31.3 + - - -
56G ASN 4.0 1.3 - - - -
57G LEU* 3.2 21.6 - - - +
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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