Contacts of the strand formed by residues 38 - 47 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225G PRO* 6.6 0.4 - - + -
227G LYS* 5.1 6.7 - - - +
32H GLY* 3.1 2.6 - - - -
33H LYS* 2.8 56.9 + - - +
36H GLU* 3.9 12.8 + - + +
37H GLY* 1.3 81.1 - - - +
39H GLN* 1.3 63.7 + - - +
69H PHE* 3.6 3.8 - - - -
214H HIS* 4.1 16.2 - - + +
215H GLU 3.6 3.4 - - - -
216H VAL* 4.1 18.4 - - + -
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Residues in contact with GLN 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11H MET* 3.2 23.5 - - + +
31H GLU 3.7 7.6 - - - +
32H GLY* 4.0 0.4 - - - -
38H THR* 1.3 79.3 - - - +
40H THR* 1.3 61.5 + - - +
41H MET* 4.7 1.2 - - - +
63H NRQ 3.5 27.1 - - + +
66H SER* 2.8 52.7 + - - -
69H PHE* 3.3 20.3 + - + +
214H HIS* 2.8 25.5 + - - -
215H GLU* 3.1 40.0 + - - +
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Residues in contact with THR 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H MET* 4.2 2.6 - - - +
30H GLY* 3.4 20.0 - - - -
31H GLU* 3.2 26.0 + - - -
39H GLN* 1.3 71.6 - - - +
41H MET* 1.3 77.2 + - - +
42H ARG* 4.2 11.4 - - - +
202H ILE* 5.8 2.9 - - + -
212H GLU* 4.1 26.2 - - + +
213H GLN 3.0 13.2 - - - +
214H HIS* 3.4 18.1 + - + +
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Residues in contact with MET 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H MET* 3.5 37.9 - - + +
13H LEU* 4.9 3.6 - - + -
28H SER* 3.4 23.1 - - - +
29H GLU 3.6 22.2 - - - +
30H GLY* 3.6 0.9 - - - +
39H GLN* 4.7 2.9 - - - +
40H THR* 1.3 74.0 - - - +
42H ARG* 1.3 62.0 + - - +
43H ILE* 3.8 17.9 - - + +
62H PHE* 3.6 29.6 - - + +
63H NRQ 3.3 26.2 - - + -
117H TYR* 4.8 4.7 - - - -
211H VAL 3.3 4.9 - - - +
212H GLU* 3.3 1.9 - - - -
213H GLN* 2.7 40.0 + - + +
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Residues in contact with ARG 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28H SER* 3.2 20.0 - - - -
29H GLU* 2.4 58.2 + - + +
30H GLY* 3.7 9.1 - - - -
31H GLU* 2.4 37.4 + - - -
40H THR* 4.2 14.0 - - + +
41H MET* 1.3 71.4 - - - +
43H ILE* 1.3 62.2 + - - +
44H LYS* 5.1 2.5 - - - +
210H TYR* 3.0 30.3 - - + +
211H VAL 3.5 4.3 - - - -
212H GLU* 3.7 24.6 + - + -
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Residues in contact with ILE 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H CYS* 4.5 3.1 - - + -
27H THR 3.5 7.2 - - - +
28H SER* 3.8 6.7 - - - -
41H MET* 4.1 7.4 - - + +
42H ARG* 1.3 76.9 - - - +
44H LYS* 1.3 74.7 + - - +
45H VAL 4.8 0.2 - - - +
55H PHE* 3.7 25.6 - - + -
62H PHE* 3.5 49.1 - - + -
209H THR 5.6 0.4 - - - +
210H TYR* 3.0 24.0 - - - -
211H VAL* 2.7 50.6 + - + +
213H GLN* 4.0 16.2 - - + +
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Residues in contact with LYS 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26H CYS* 3.3 3.8 - - - +
27H THR* 2.7 49.2 + - - +
42H ARG 5.1 2.7 - - - +
43H ILE* 1.3 80.1 - - - +
45H VAL* 1.3 64.2 + - - +
46H VAL* 3.5 11.1 + - + +
209H THR* 3.4 11.0 + - - -
210H TYR* 3.1 44.3 - - + +
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Residues in contact with VAL 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H LYS 3.8 6.5 - - - +
26H CYS* 3.8 16.6 - - - -
43H ILE* 4.8 0.2 - - - +
44H LYS* 1.3 75.3 - - - +
46H VAL* 1.3 59.9 + - - +
47H GLU 3.3 24.5 - - - +
49H GLY* 3.5 24.7 - - - +
51H LEU* 4.0 28.9 - - + -
55H PHE* 4.6 7.6 - - + -
208H GLU 4.2 2.7 - - - +
209H THR* 2.8 41.4 + - + +
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Residues in contact with VAL 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H LYS* 3.1 32.1 + - + +
26H CYS* 3.8 4.0 - - - +
27H THR* 3.7 33.0 - - + +
44H LYS* 3.7 17.7 - - + +
45H VAL* 1.3 77.7 - - - +
47H GLU* 1.3 64.0 + - + +
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Residues in contact with GLU 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23H HIS* 4.0 23.4 + - + +
24H PHE* 3.5 2.5 - - - -
25H LYS* 3.2 53.3 + - + +
45H VAL* 3.3 9.7 - - - +
46H VAL* 1.3 80.5 - - - +
48H GLY* 1.3 60.8 + - - +
49H GLY 2.9 11.3 + - - -
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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