Contacts of the strand formed by residues 28 - 36 (chain A) in PDB entry 4FZY
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASP 3.4 1.6 - - - +
24A VAL* 3.3 3.7 - - - +
25A ILE* 2.8 36.5 + - - +
26A ASP 4.2 3.4 - - - +
27A GLY* 1.3 81.8 - - - +
29A ILE* 1.3 68.0 + - - +
30A VAL* 3.7 25.2 + - + +
148A ILE* 4.7 0.2 - - - +
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Residues in contact with ILE 29 (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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22A VAL* 3.7 26.9 - - + -
23A ASP 3.2 4.9 - - - +
24A VAL* 4.2 2.7 - - + -
28A LYS* 1.3 78.6 - - - +
30A VAL* 1.3 69.2 + - - +
32A PRO* 5.7 0.4 - - + +
125A VAL* 4.2 23.6 - - + -
141A TYR* 3.6 30.7 - - + +
144A ALA* 3.9 21.1 - - + -
145A ALA* 4.6 3.1 - - - +
148A ILE* 3.9 22.4 - - + -
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Residues in contact with VAL 30 (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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22A VAL* 3.7 2.1 - - - +
23A ASP* 2.6 53.1 + - + +
25A ILE* 4.5 21.1 - - + -
28A LYS* 3.8 33.4 - - + +
29A ILE* 1.3 80.2 - - - +
31A ASN* 1.3 72.8 + - + +
32A PRO* 3.4 7.2 - - - +
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Residues in contact with ASN 31 (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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3A ARG* 3.5 13.7 - - - +
21A SER* 4.0 1.4 + - - +
22A VAL* 4.0 7.1 - - - -
23A ASP* 2.9 27.3 + - - +
30A VAL* 1.3 86.3 - - + +
32A PRO* 1.3 73.0 - - - +
33A MET* 3.5 19.7 + - - +
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Residues in contact with PRO 32 (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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21A SER 3.4 7.9 - - - +
22A VAL* 3.9 10.1 - - + -
30A VAL* 3.4 6.5 - - - -
31A ASN* 1.3 94.2 - - - +
33A MET* 1.3 63.1 + - - +
137A LEU* 4.3 12.8 - - + -
141A TYR* 3.4 26.0 - - - +
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Residues in contact with MET 33 (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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3A ARG* 3.8 25.6 - - - +
20A ALA* 3.0 5.2 - - - +
21A SER* 2.7 57.3 + - - +
31A ASN* 3.9 18.6 - - - +
32A PRO* 1.3 80.2 - - - +
34A SER* 1.3 59.3 + - - +
35A HIS* 4.7 6.1 - - + -
70A HIS* 3.5 37.2 - - - +
71A TYR* 3.7 20.4 - - + +
137A LEU* 3.9 4.4 - - - +
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Residues in contact with SER 34 (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* 5.2 7.9 + - - -
19A ILE 3.1 6.7 - - - -
20A ALA* 3.4 16.8 - - - -
33A MET* 1.3 78.1 - - - +
35A HIS* 1.3 76.1 + - - +
71A TYR* 3.2 2.2 - - - -
137A LEU* 3.7 25.7 - - - +
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Residues in contact with HIS 35 (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* 3.3 5.8 - - - +
19A ILE* 2.7 37.5 + - + +
33A MET* 4.7 6.3 - - + -
34A SER* 1.3 84.4 + - - +
36A LEU* 1.3 68.1 - - - +
37A VAL* 3.7 1.8 - - + +
62A PRO* 5.9 1.1 - - + -
67A VAL* 3.9 30.7 - - + +
70A HIS* 4.1 27.6 + + + -
71A TYR* 2.7 40.0 + + - -
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Residues in contact with LEU 36 (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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17A VAL 3.6 14.8 - - - +
18A GLU* 3.9 11.4 - - + +
35A HIS* 1.3 78.1 - - - +
37A VAL* 1.3 59.9 + - - +
53A ILE* 4.1 12.3 - - + -
57A MET* 4.0 19.7 - - + +
58A VAL* 3.9 11.0 - - + -
61A LYS* 3.5 48.5 - - + +
62A PRO* 4.2 7.6 - - - +
135A ARG* 3.6 29.6 - - - +
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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