Contacts of the strand formed by residues 43 - 51 (chain O) in PDB entry 3HOU
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 43 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41O ILE* 5.0 0.2 - - - +
42O PRO* 1.3 78.7 + - - +
44O LEU* 1.3 87.6 + - - +
45O ALA* 4.8 1.3 - - + -
74O SER* 3.7 14.0 + - - +
77O ILE* 3.7 8.0 - - - +
161O LYS* 3.2 5.2 - - - +
162O GLY 2.8 30.1 + - - -
169O LYS 4.8 2.5 - - - +
170O TRP* 3.1 36.8 + - + +
171O GLY 5.1 1.3 - - - +
172O PRO* 3.6 21.8 - - - +
237O SER* 3.9 14.3 + - - +
238O ILE* 5.2 1.7 - - - +
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Residues in contact with LEU 44 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O THR* 1.3 89.4 - - - +
45O ALA* 1.3 63.1 + - - +
72O LEU* 3.5 35.5 + - + +
73O GLN 4.0 2.5 - - - +
74O SER* 2.9 15.8 + - - +
77O ILE* 3.7 13.2 - - + -
80O LEU* 3.8 17.0 - - + -
97O VAL* 3.4 30.5 - - + -
129O ILE* 3.6 15.3 - - + -
130O GLY* 4.0 9.6 - - - +
159O ALA* 3.1 30.1 - - + -
160O LYS 3.4 8.3 - - - +
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Residues in contact with ALA 45 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43O THR* 4.8 1.1 - - + -
44O LEU* 1.3 77.6 - - - +
46O ILE* 1.3 66.8 + - - +
47O ASP* 3.4 4.0 + - - +
68O GLY 3.9 17.7 - - - +
70O ILE 5.2 2.0 - - - +
71O PRO* 6.5 0.2 - - + -
72O LEU* 3.7 8.7 - - + -
159O ALA* 3.7 5.4 - - - -
160O LYS 3.0 26.0 + - - +
169O LYS* 4.1 18.6 - - + +
170O TRP* 3.7 19.8 + - + +
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Residues in contact with ILE 46 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O ALA* 1.3 72.4 - - - +
47O ASP* 1.3 60.6 + - - +
48O SER 4.0 3.1 - - - +
49O VAL* 3.8 26.5 - - + -
67O LEU* 3.4 39.2 + - + +
68O GLY* 3.7 2.3 + - - -
70O ILE* 5.8 0.2 - - + -
72O LEU* 3.4 20.2 - - + +
99O LEU* 4.9 6.1 - - + -
118O LEU* 4.9 14.4 - - + -
157O CYS* 3.5 38.1 - - + -
158O VAL 4.5 0.4 - - - +
159O ALA* 3.7 11.0 - - + +
169O LYS* 3.0 21.7 + - - +
69X ALA* 3.3 11.0 - - + +
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Residues in contact with ASP 47 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O ALA 3.4 3.1 + - - +
46O ILE* 1.3 73.6 - - - +
48O SER* 1.3 66.5 + - - +
158O VAL 3.4 13.5 + - - +
160O LYS* 4.4 21.1 + - + +
169O LYS* 2.8 16.7 + - - +
170O TRP* 3.7 19.5 - - + -
67X PHE 4.4 0.5 - - - +
68X GLU* 4.9 2.1 - - - -
69X ALA* 3.2 13.4 + - - -
70X ARG* 2.6 39.6 + - - -
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Residues in contact with SER 48 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O ILE* 4.0 0.4 - - - +
47O ASP* 1.3 82.1 - - - +
49O VAL* 1.3 61.5 + - - +
50O GLU* 4.0 0.6 + - - +
156O THR 3.6 0.7 - - - +
157O CYS* 3.4 5.9 - - - +
158O VAL* 3.1 46.2 + - - +
160O LYS* 5.2 6.7 - - - -
66X GLN* 3.4 31.5 + - - +
67X PHE 3.2 9.6 - - - -
69X ALA* 3.5 4.8 - - - +
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Residues in contact with VAL 49 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46O ILE* 3.8 18.2 - - + -
48O SER* 1.3 78.9 + - - +
50O GLU* 1.3 61.4 + - - +
51O VAL* 3.3 24.0 + - + -
64O ALA* 4.2 24.2 - - + -
67O LEU* 3.8 32.5 - - + -
155O LEU* 4.4 8.5 - - + -
156O THR 3.3 7.6 - - - +
157O CYS* 4.1 4.0 - - - -
66X GLN* 4.3 1.1 - - - -
67X PHE* 3.0 35.8 + - - +
69X ALA* 4.5 4.5 - - + -
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Residues in contact with GLU 50 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O SER* 4.0 2.2 + - - +
49O VAL* 1.3 71.2 - - - +
51O VAL* 1.3 59.4 + - - +
52O GLU* 3.6 1.4 + - - +
155O LEU* 3.6 1.7 - - - -
156O THR* 3.0 52.9 + - - +
64X LEU* 2.7 45.7 - - + +
65X VAL 3.3 8.7 - - - +
66X GLN* 4.1 10.7 - - + +
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Residues in contact with VAL 51 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O VAL* 3.3 17.2 + - + +
50O GLU* 1.3 71.2 - - - +
52O GLU* 1.3 63.1 + - - +
53O THR 3.8 10.5 - - - +
54O ASN* 4.1 12.1 - - + -
60O ASP* 3.4 36.1 - - + +
63O ILE* 6.5 0.4 - - + -
64O ALA* 6.0 0.2 - - + -
154O LYS 4.0 2.0 - - - -
155O LEU* 3.3 28.0 - - + -
60X ARG* 3.5 12.6 + - - +
64X LEU* 3.9 5.2 - - - +
65X VAL* 2.9 36.7 + - + +
67X PHE* 4.4 7.6 - - + -
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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