Contacts of the strand formed by residues 38 - 47 (chain C) in PDB entry 3BXB
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 THR 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C GLY* 3.3 1.1 - - - -
33C LYS* 2.8 52.7 + - - +
36C GLU* 4.4 14.1 + - + +
37C GLY* 1.3 85.3 - - - +
39C GLN* 1.3 60.9 + - - +
69C PHE* 3.9 2.5 - - - -
214C HIS* 4.0 17.0 - - + +
215C GLU 3.4 4.0 - - - -
216C VAL* 3.7 22.7 - - + -
225D PRO* 6.1 2.2 - - + -
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Residues in contact with GLN 39 (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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11C MET* 4.1 9.7 - - + +
31C GLU 3.6 10.8 - - - +
32C GLY* 3.9 0.9 - - - -
38C THR* 1.3 77.4 - - - +
40C THR* 1.3 62.0 + - - +
41C MET* 4.8 0.2 - - - +
63C NRQ 3.4 16.4 - - + +
66C SER* 2.7 52.1 + - - -
69C PHE* 3.3 29.3 + - + +
214C HIS* 3.0 18.7 + - - -
215C GLU* 3.0 54.0 + - + +
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Residues in contact with THR 40 (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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11C MET* 3.0 20.2 - - - +
30C GLY* 3.2 0.4 - - - -
31C GLU* 2.9 32.1 + - - +
39C GLN* 1.3 73.1 - - - +
41C MET* 1.3 64.8 + - - +
42C ARG* 3.5 25.8 - - - +
63C NRQ 4.1 1.6 - - - -
202C ILE* 5.8 0.4 - - + +
212C GLU* 4.2 20.9 - - + +
213C GLN 3.6 9.4 - - - +
214C HIS* 3.2 23.1 + - + +
227D LYS* 4.6 6.8 + - - -
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Residues in contact with MET 41 (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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11C MET* 3.4 37.2 - - + +
13C LEU* 4.7 1.6 - - + -
28C SER* 3.4 26.7 - - - +
29C GLU 3.4 15.9 - - - +
30C GLY* 4.1 0.7 - - - +
39C GLN* 4.8 1.6 - - - +
40C THR* 1.3 72.6 - - - +
42C ARG* 1.3 61.8 + - - +
43C ILE* 4.0 7.2 - - + +
62C PHE* 3.1 54.5 - - + +
63C NRQ 3.6 17.7 - - + -
117C TYR* 4.6 5.6 - - - -
211C VAL 3.6 1.7 - - - +
212C GLU* 3.3 4.7 - - - +
213C GLN* 3.0 33.4 + - - +
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Residues in contact with ARG 42 (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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28C SER* 3.1 21.0 - - - -
29C GLU* 2.7 26.0 + - + +
30C GLY* 3.8 14.4 - - - +
31C GLU* 2.6 44.4 + - - -
40C THR* 3.5 19.0 - - - +
41C MET* 1.3 70.7 - - - +
43C ILE* 1.3 62.1 + - - +
44C LYS* 4.1 3.0 + - - +
210C TYR* 3.4 29.2 - - + +
211C VAL 3.6 3.4 - - - -
212C GLU* 3.6 24.1 + - + -
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Residues in contact with ILE 43 (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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26C CYS* 4.5 1.8 - - + -
27C THR 3.9 5.8 - - - +
28C SER* 3.5 20.2 - - - +
41C MET* 4.3 7.4 - - + +
42C ARG* 1.3 74.3 - - - +
44C LYS* 1.3 72.1 + - - +
45C VAL* 6.0 0.2 - - - -
55C PHE* 3.7 20.6 - - + -
62C PHE* 3.4 44.0 - - + -
209C THR 3.7 0.5 - - - +
210C TYR* 3.3 10.6 - - - -
211C VAL* 2.6 44.8 + - + +
213C GLN* 3.8 40.6 - - + +
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Residues in contact with LYS 44 (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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26C CYS* 3.4 7.6 - - - +
27C THR* 3.0 40.5 + - - +
29C GLU* 6.1 3.6 - - - +
42C ARG 4.1 2.9 + - - +
43C ILE* 1.3 78.8 - - - +
45C VAL* 1.3 62.2 + - - +
46C VAL* 3.8 17.1 + - + +
209C THR 3.4 4.9 - - - +
210C TYR* 4.1 22.9 - - + -
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Residues in contact with VAL 45 (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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24C PHE* 4.9 0.2 - - + -
25C LYS 3.6 7.0 - - - +
26C CYS* 4.0 10.8 - - - -
43C ILE* 5.6 0.2 - - + -
44C LYS* 1.3 75.4 - - - +
46C VAL* 1.3 61.0 + - - +
47C GLU 3.1 24.9 - - - +
49C GLY* 3.7 19.8 - - - +
51C LEU* 3.9 33.0 - - + -
55C PHE* 4.3 7.2 - - + -
208C GLU 3.9 6.1 - - - +
209C THR* 2.8 42.2 + - + +
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Residues in contact with VAL 46 (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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25C LYS* 2.8 37.9 + - + +
26C CYS* 4.1 5.4 - - - +
27C THR* 4.0 29.6 - - + +
44C LYS* 4.0 16.4 - - + +
45C VAL* 1.3 78.9 - - - +
47C GLU* 1.3 62.3 + - + +
49C GLY 5.5 0.4 - - - -
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Residues in contact with GLU 47 (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 HIS* 3.4 27.3 + - - +
24C PHE* 3.6 3.8 - - - -
25C LYS* 3.4 42.9 + - + +
45C VAL* 3.1 13.7 - - - +
46C VAL* 1.3 78.3 - - - +
48C GLY* 1.3 60.2 + - - +
49C GLY 2.8 12.5 + - - -
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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