Contacts of the strand formed by residues 31 - 38 (chain C) in PDB entry 3U8Z
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 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A MET* 5.7 1.8 - - + -
34A GLU 3.6 7.9 - - - +
35A PHE* 3.6 31.6 - - + -
53A THR* 4.2 11.4 - - + -
27C VAL* 3.6 5.6 - - - +
28C THR* 2.7 46.6 + - + +
30C ASP* 1.3 81.7 + - - +
32C GLU* 1.3 61.7 + - - +
33C MET* 6.3 0.9 - - + -
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Residues in contact with GLU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A GLU* 4.5 3.8 - - - +
33A MET* 3.1 9.7 - - - +
34A GLU* 2.8 69.4 + - + +
25C ARG* 3.1 46.5 - - + +
26C ILE 3.6 4.7 - - - +
27C VAL* 4.5 7.2 - - + +
31C ALA* 1.3 76.3 - - - +
33C MET* 1.3 67.8 + - - +
34C GLU* 3.2 36.0 - - - +
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Residues in contact with MET 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 4.2 2.9 - - + -
32A GLU 3.4 9.4 - - - +
33A MET* 3.9 20.4 - - + +
53A THR* 6.4 0.9 - - - -
24C VAL 3.7 0.5 - - - +
25C ARG* 3.6 0.7 - - - -
26C ILE* 2.7 56.5 + - + +
28C THR* 3.7 26.5 - - + -
31C ALA* 5.8 1.3 - - + -
32C GLU* 1.3 80.6 - - - +
34C GLU* 1.3 57.9 + - - +
35C PHE* 3.5 26.9 - - + -
50C VAL* 3.6 30.7 - - + +
53C THR* 4.0 14.4 - - - -
54C LEU* 3.9 19.7 - - + -
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Residues in contact with GLU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ALA* 3.6 20.8 - - - +
32A GLU* 2.9 49.3 + - + +
23C THR* 3.8 28.6 - - + +
24C VAL 3.3 6.1 - - - +
25C ARG* 4.2 15.7 + - - +
32C GLU* 3.2 22.7 + - - +
33C MET* 1.3 72.7 - - - +
35C PHE* 1.3 60.3 + - - +
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Residues in contact with PHE 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ASP 4.7 7.6 - - - -
31A ALA* 4.0 13.0 - - + -
23C THR* 3.5 5.8 - - - +
24C VAL* 2.9 33.9 + - + +
26C ILE* 3.6 29.4 - - + -
33C MET* 3.5 46.0 - - + -
34C GLU* 1.3 76.3 - - - +
36C ASN* 1.3 66.1 + - - +
37C CYS 3.6 0.6 + - - -
46C LEU* 4.7 10.5 - - + -
49C LEU* 3.6 35.9 - - + -
50C VAL* 3.8 15.0 - - + -
53C THR* 3.2 28.3 - - + -
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Residues in contact with ASN 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C THR* 4.1 26.8 + - + +
22C PHE 3.7 5.6 - - - +
23C THR* 3.9 16.4 + - - -
34C GLU 6.1 0.2 - - - -
35C PHE* 1.3 72.2 - - - +
37C CYS* 1.3 61.4 + - - +
38C GLU* 3.9 2.3 + - - +
41C TRP* 4.3 10.9 - - - -
49C LEU* 4.8 3.8 - - - +
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Residues in contact with CYS 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C THR* 3.2 1.5 - - - -
22C PHE* 2.8 53.6 + - + +
24C VAL* 3.5 27.6 - - + -
35C PHE* 3.6 1.8 + - - +
36C ASN* 1.3 72.0 - - - +
38C GLU* 1.3 77.1 + - - +
41C TRP* 3.7 28.0 - - + -
46C LEU* 4.4 16.2 - - + -
81C VAL* 4.2 13.7 - - - -
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Residues in contact with GLU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LYS* 5.7 4.9 - - - -
20C LYS 3.5 8.7 - - - -
21C THR* 3.9 15.9 - - + -
22C PHE* 3.6 2.8 - - - -
36C ASN 3.9 2.1 + - - +
37C CYS* 1.3 80.9 - - - +
39C MET* 1.3 65.2 + - - +
40C LYS* 3.3 1.8 - - + +
41C TRP* 3.2 66.3 + - + +
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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