Contacts of the strand formed by residues 31 - 37 (chain C) in PDB entry 3BYB
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 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLU* 2.9 31.2 + - - +
25C TYR* 3.6 9.7 - - - -
26C ASN* 2.8 29.3 + - - +
29C GLU* 3.9 29.8 + - + +
30C LYS* 1.3 79.3 - - - +
32C CYS* 1.3 62.2 + - - +
33C LEU* 3.6 19.7 - - + -
50C LYS* 5.6 8.5 - - - +
54C GLU* 6.1 0.4 - - - +
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Residues in contact with CYS 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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23C PHE* 4.8 3.0 - - + -
24C TYR 3.3 4.0 - - - -
25C TYR* 3.9 13.0 - - - -
31C LYS* 1.3 75.9 - - - +
33C LEU* 1.3 64.7 + - - +
50C LYS* 3.7 31.1 + - + +
53C CYS* 2.1 65.3 - - + -
54C GLU* 3.5 25.4 + - + +
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Residues in contact with LEU 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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26A ASN* 4.3 4.5 - - - +
29A GLU* 3.5 36.6 - - + +
33A LEU* 3.5 32.1 - - + -
23C PHE* 3.2 7.0 - - - -
24C TYR* 2.8 50.7 + - + +
26C ASN* 3.7 20.4 - - + -
29C GLU* 4.9 2.5 - - + -
31C LYS* 3.6 30.1 - - + +
32C CYS* 1.3 77.9 - - - +
34C GLU* 1.3 67.6 + - - +
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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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24A TYR* 5.0 0.3 + - - -
26A ASN* 4.5 10.6 + - - -
21C PRO* 3.5 21.9 - - - +
22C SER 3.3 14.6 - - - +
23C PHE* 3.6 27.4 - - + -
24C TYR* 4.5 1.7 - - - -
33C LEU* 1.3 79.7 - - - +
35C PHE* 1.3 70.4 + - - +
36C ILE* 4.8 8.0 - - + +
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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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11A ALA* 5.7 7.6 - - + -
24A TYR* 5.0 5.2 - - + +
11C ALA* 4.1 15.7 - - + -
12C ASP 3.6 27.4 - - - -
13C THR* 4.2 7.0 - - + -
20C PHE 3.6 0.5 - - - +
21C PRO* 3.7 0.9 - - - +
22C SER* 2.8 50.7 + - - +
23C PHE 3.7 21.8 - - - -
24C TYR* 3.6 31.9 - + + -
34C GLU* 1.3 76.7 - - - +
36C ILE* 1.3 84.8 + - - +
37C TYR* 4.1 13.9 - - + -
45C ASN 4.6 6.1 - - - -
46C ASN* 3.9 23.3 - - - -
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Residues in contact with ILE 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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10A PRO* 3.9 30.2 - - + +
11A ALA* 4.3 2.4 + - - +
13C THR* 3.3 24.8 - - - +
18C VAL* 3.5 18.5 - - + +
19C ARG* 3.4 29.4 - - - +
20C PHE 3.3 12.1 - - - +
21C PRO* 4.5 9.4 - - + -
34C GLU* 4.8 9.9 - - + +
35C PHE* 1.3 84.8 - - - +
37C TYR* 1.3 58.0 + - - +
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Residues in contact with TYR 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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12C ASP 4.0 6.3 - - - -
13C THR* 3.3 29.2 - - - -
18C VAL* 4.1 0.9 - - - -
19C ARG 3.0 5.5 + - - -
20C PHE* 2.8 37.0 + + + +
22C SER* 3.3 32.5 - - - +
35C PHE* 4.1 7.6 - + + -
36C ILE* 1.3 74.6 - - - +
38C GLY* 1.3 59.8 + - - +
39C GLY* 3.3 33.4 + - - -
40C CYS 3.2 18.1 + - - -
41C GLU 2.6 29.0 + - - -
46C ASN* 3.3 31.1 + - - -
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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