Contacts of the strand formed by residues 32 - 39 (chain A) in PDB entry 4PBZ
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 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TRP* 2.8 33.1 + + - -
28A THR* 3.1 27.1 + - + +
29A PRO* 3.9 10.9 - - - +
30A PHE 3.5 1.0 + - - -
31A LEU* 1.3 99.2 - - + +
33A ASP* 1.3 64.4 + - - +
34A LEU 3.6 10.8 - - - +
35A VAL* 3.2 33.2 - - + -
368A PHE* 3.6 17.1 - + - -
369A ILE 4.7 0.5 + - - -
370A HIS* 2.6 33.7 + + - -
402A TRP* 3.6 31.4 - + + -
403A GLN 3.3 11.2 - - - -
404A MET* 4.3 0.7 - - - -
405A ALA* 4.1 2.5 - - - +
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Residues in contact with ASP 33 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TYR* 1.3 74.5 - - - +
34A LEU* 1.3 63.4 + - - +
403A GLN* 2.8 26.6 + - - +
404A MET 3.8 2.4 - - - +
405A ALA* 3.7 16.6 - - - +
406A GLU* 3.0 31.4 + - - +
409A TYR* 4.8 1.6 + - - -
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Residues in contact with LEU 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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32A TYR* 3.3 0.9 - - - +
33A ASP* 1.3 84.1 - - - +
35A VAL* 1.3 72.1 + - - +
36A MET* 4.1 17.7 - - + -
86A LEU* 3.9 24.9 - - + -
87A PRO* 4.1 28.3 - - + -
389A VAL* 4.7 8.5 - - + -
401A VAL* 4.3 20.0 - - + +
402A TRP* 3.2 6.7 - - - +
403A GLN* 2.9 44.7 + - + +
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Residues in contact with VAL 35 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A TRP* 4.0 26.9 - - + -
25A LYS* 5.5 8.6 + - - +
28A THR* 4.3 12.8 - - + -
32A TYR* 3.2 46.2 - - + -
34A LEU* 1.3 74.3 - - - +
36A MET* 1.3 67.1 + - - +
37A THR* 4.2 12.0 + - - +
370A HIS* 5.4 0.2 - - + -
400A GLN* 5.1 4.9 - - + -
401A VAL 3.6 4.3 - - - -
402A TRP* 4.2 8.3 - - + -
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Residues in contact with MET 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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34A LEU* 4.1 19.3 - - + -
35A VAL* 1.3 77.0 - - - +
37A THR* 1.3 61.2 + - - +
84A VAL* 4.2 9.2 - - + -
85A GLN 4.2 13.0 - - - +
86A LEU* 4.2 17.0 - - - -
87A PRO* 5.3 1.8 - - - -
114A LYS* 4.1 19.7 - - - +
115A ILE* 3.5 37.5 - - + +
399A MET 3.8 1.0 - - - +
400A GLN* 3.2 6.2 - - - +
401A VAL* 2.8 48.5 + - + +
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Residues in contact with THR 37 (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 TYR* 5.0 9.8 + - - +
24A TRP* 4.9 2.4 - - - -
25A LYS* 5.3 6.3 + - - -
35A VAL* 4.2 9.1 + - - +
36A MET* 1.3 74.3 - - - +
38A HIS* 1.3 64.5 + - - +
39A ALA 5.4 0.2 - - - +
115A ILE* 5.5 0.2 - - - -
398A ILE* 3.7 35.9 - - + -
399A MET 3.7 2.7 - - - -
400A GLN* 3.6 20.1 + - + +
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Residues in contact with HIS 38 (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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37A THR* 1.3 79.5 - - - +
39A ALA* 1.3 76.7 + - - +
40A LEU* 3.6 28.3 + - + +
115A ILE* 3.7 50.6 + - + +
117A ILE* 5.5 5.2 - - + +
398A ILE* 3.7 1.5 - - - -
399A MET* 2.9 50.4 + - + +
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Residues in contact with ALA 39 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A HIS* 1.3 86.4 + - - +
40A LEU* 1.3 67.1 + - - +
397A ASN* 3.8 9.6 - - + +
398A ILE* 4.3 17.5 - - + +
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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