Contacts of the strand formed by residues 45 - 51 (chain H) in PDB entry 5FHX
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 LEU 45 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37H ILE* 4.0 15.7 - - + -
38H LYS 3.5 0.7 - - - -
39H GLN* 3.7 41.5 - - + +
44H GLY* 1.3 71.9 + - - -
46H GLU* 1.3 60.0 - - - +
95H TYR* 4.7 2.5 - - + -
113H TRP* 4.7 2.5 - - + -
154L PHE* 5.4 1.6 - - + -
162L PRO* 4.3 27.1 - - + -
205L TYR* 4.2 27.9 - - + -
216L PHE* 3.6 63.8 + - + +
217L GLY 4.9 1.6 + - - -
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Residues in contact with GLU 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H ILE* 3.2 8.6 - - - +
38H LYS* 2.8 62.4 + - + +
43H GLN* 5.8 7.4 - - + +
44H GLY 5.8 0.2 - - - -
45H LEU* 1.3 74.1 - - - +
47H TRP* 1.3 69.4 + - - +
48H ILE 3.6 0.2 + - - -
61H ASN* 4.5 3.6 - - - +
63H ARG* 3.6 26.8 + - - +
64H PHE* 3.5 27.2 - - + -
216L PHE* 4.8 0.7 - - - -
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Residues in contact with TRP 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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35H HIS* 2.8 30.5 + - + -
36H TRP 4.0 2.2 - - - -
37H ILE* 4.2 9.6 - - + -
46H GLU* 1.3 71.4 - - - +
48H ILE* 1.3 59.9 + - - +
49H GLY* 3.7 20.2 + - - -
50H MET* 3.6 23.3 - - + -
59H ARG* 3.7 19.1 - - + -
60H LEU 4.3 0.9 - - - -
61H ASN* 2.7 56.0 + - + +
64H PHE* 3.9 2.4 - - - -
110H PHE* 4.2 8.3 - + - -
212L TYR* 3.6 28.3 - + + -
213L PRO* 3.6 31.2 - - + -
214L PHE* 3.3 44.8 + + + +
216L PHE* 4.6 7.2 - + + -
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Residues in contact with ILE 48 (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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36H TRP* 2.8 28.9 + - + +
37H ILE 3.6 5.6 - - - +
38H LYS* 3.6 23.1 - - + +
47H TRP* 1.3 73.9 - - - +
49H GLY* 1.3 58.0 + - - +
60H LEU* 3.7 8.0 - - + +
61H ASN* 2.9 27.9 + - - +
64H PHE* 3.8 33.9 - - + -
68H ALA* 4.0 27.4 - - + -
70H LEU* 5.1 2.0 - - + -
81H MET* 4.2 10.1 - - - -
94H TYR* 3.5 37.2 - - + -
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Residues in contact with GLY 49 (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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35H HIS* 3.3 6.1 - - - +
36H TRP* 2.9 26.3 + - - +
47H TRP* 3.7 17.2 + - - -
48H ILE* 1.3 81.2 - - - +
50H MET* 1.3 60.7 - - - +
59H ARG 3.1 13.7 - - - -
60H LEU* 4.1 2.2 - - - -
70H LEU* 3.8 12.1 - - - -
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Residues in contact with MET 50 (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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73A PHE* 3.8 19.5 - - + -
74A HIS* 4.4 1.1 - - - -
33H TRP* 3.4 24.0 - - + -
34H ILE 3.2 11.0 - - - +
35H HIS* 3.4 38.8 - - + +
47H TRP* 3.6 8.3 - - + -
49H GLY* 1.3 72.5 - - - -
51H ILE* 1.4 61.1 + - - +
58H THR* 3.4 1.7 - - - -
59H ARG* 2.9 67.2 + - + +
70H LEU* 3.3 13.7 - - - +
212L TYR* 3.6 28.9 - - + +
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Residues in contact with ILE 51 (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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33H TRP* 3.3 7.4 - - - -
34H ILE* 2.8 50.8 + - + +
36H TRP* 4.9 4.3 - - - +
50H MET* 1.4 75.5 - - - +
52H ASP* 1.3 59.1 + - - +
53H PRO* 3.3 5.2 - - - +
56H GLY* 4.1 15.3 - - - +
57H GLU 3.3 16.2 - - - +
58H THR* 3.5 8.5 - - - +
70H LEU* 3.3 43.1 - - + +
71H THR* 3.5 19.5 - - - +
72H VAL* 3.8 23.6 - - + +
79H ALA* 4.9 2.5 - - + -
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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