Contacts of the strand formed by residues 38 - 47 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32G GLY* 3.3 1.1 - - - -
33G LYS* 2.8 50.7 + - - +
36G GLU* 3.7 21.3 + - + +
37G GLY* 1.3 83.1 - - - +
39G GLN* 1.3 65.9 + - - +
69G PHE* 3.4 6.8 - - - -
214G HIS* 4.1 17.9 - - + +
215G GLU 3.4 4.0 - - - -
216G VAL* 4.3 15.7 - - + -
225H PRO* 6.5 0.2 - - + -
227H LYS* 6.1 0.7 - - - +
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Residues in contact with GLN 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G MET* 3.8 18.7 - - + +
31G GLU 3.8 7.0 - - - -
32G GLY* 3.8 1.1 - - - -
38G THR* 1.3 78.2 - - - +
40G THR* 1.3 62.7 + - - +
41G MET* 4.8 0.3 - - - +
63G NRQ 3.6 20.9 - - + +
66G SER* 2.9 41.1 + - - -
69G PHE* 3.2 32.5 + - + +
70G ILE* 5.6 0.6 - - - +
213G GLN 3.8 0.2 - - - +
214G HIS* 3.1 9.3 + - - -
215G GLU* 2.8 64.0 + - + +
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Residues in contact with THR 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G MET* 3.3 5.9 - - - +
30G GLY* 3.2 3.0 - - - -
31G GLU* 3.0 45.1 + - - +
39G GLN* 1.3 75.1 - - - +
41G MET* 1.3 65.1 + - - +
42G ARG* 4.3 11.2 - - - +
202G ILE* 4.9 6.1 - - + -
212G GLU* 4.1 26.0 - - + +
213G GLN 3.2 11.4 - - - +
214G HIS* 3.5 15.7 + - + +
227H LYS* 5.6 0.9 - - - -
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Residues in contact with MET 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G MET* 3.5 38.6 - - + +
13G LEU* 4.2 13.5 - - + -
28G SER* 3.0 30.7 - - - +
29G GLU 3.8 5.6 - - - -
30G GLY* 4.1 9.0 - - - +
39G GLN* 5.1 0.2 - - - +
40G THR* 1.3 80.0 - - - +
42G ARG* 1.3 63.9 + - - +
43G ILE* 4.0 15.9 - - + +
62G PHE* 4.0 32.3 - - - +
63G NRQ 3.7 18.2 - - + -
117G TYR* 4.8 2.7 - - + -
211G VAL 3.7 1.6 - - - +
212G GLU* 3.2 5.9 - - - +
213G GLN 2.9 31.6 + - - +
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Residues in contact with ARG 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G HIS* 5.4 3.0 + - - -
27G THR 4.0 0.2 - - - +
28G SER* 3.0 21.0 - - - -
29G GLU* 2.9 29.0 + - + +
30G GLY* 3.2 24.4 - - - +
31G GLU* 2.7 40.9 + - - -
40G THR* 4.3 11.3 - - + +
41G MET* 1.3 73.6 - - - +
43G ILE* 1.3 61.1 - - - +
44G LYS* 4.1 2.8 + - - +
210G TYR* 3.3 24.2 - - + +
211G VAL 3.6 3.6 - - - -
212G GLU* 3.4 29.1 + - + +
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Residues in contact with ILE 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G CYS* 4.5 2.7 - - + -
27G THR 3.4 5.8 - - - +
28G SER* 3.3 19.5 - - - +
41G MET* 4.0 19.5 - - + +
42G ARG* 1.3 71.3 - - - +
44G LYS* 1.3 71.9 + - - +
45G VAL* 5.3 0.7 - - + -
55G PHE* 3.6 31.2 - - + -
62G PHE* 3.7 41.5 - - + -
209G THR 3.8 0.3 - - - +
210G TYR* 3.2 10.8 - - - -
211G VAL* 2.6 49.5 + - + +
213G GLN* 4.2 19.7 - - + +
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Residues in contact with LYS 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G CYS* 3.2 5.7 - - - +
27G THR* 2.8 51.7 + - - +
42G ARG 5.0 3.1 - - - +
43G ILE* 1.3 78.8 - - - +
45G VAL* 1.3 61.5 + - - +
46G VAL* 3.4 12.6 + - + -
209G THR 3.6 5.8 - - - +
210G TYR* 4.1 20.4 - - + -
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Residues in contact with VAL 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G LYS 3.5 11.7 - - - +
26G CYS* 4.3 10.1 - - - -
43G ILE* 5.3 0.4 - - + -
44G LYS* 1.3 72.0 - - - +
46G VAL* 1.3 60.3 + - - +
47G GLU 3.4 3.8 + - - +
49G GLY* 3.6 35.1 - - - +
51G LEU* 3.7 34.1 - - + -
55G PHE* 4.4 6.1 - - + -
208G GLU 3.6 23.8 - - - +
209G THR* 2.9 26.2 + - - +
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Residues in contact with VAL 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G LYS* 3.0 33.6 + - + +
26G CYS 4.4 1.3 - - - +
27G THR* 3.4 37.0 - - + +
44G LYS* 3.4 14.8 + - + +
45G VAL* 1.3 72.8 - - - +
47G GLU* 1.3 63.8 + - + +
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Residues in contact with GLU 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23G HIS* 4.0 21.5 + - + +
24G PHE* 3.1 8.0 - - - +
25G LYS* 2.9 68.2 + - + +
45G VAL* 3.3 3.2 + - - +
46G VAL* 1.3 82.0 - - + +
48G GLY* 1.3 65.7 + - - +
49G GLY 3.2 2.7 + - - +
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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