Contacts of the strand formed by residues 32 - 39 (chain D) in PDB entry 1H4O
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 LYS 32 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113C ASP* 4.3 15.7 + - - -
145C ASP* 3.7 15.6 - - - +
27D GLU 5.5 0.9 - - - -
28D LEU* 3.7 18.9 + - - +
29D PHE* 3.3 17.0 - - - +
30D LYS 3.2 16.6 - - - +
31D GLY* 1.3 81.1 - - - +
33D LYS* 1.3 65.4 + - - +
68D GLN* 3.7 34.4 + - + +
69D VAL* 3.9 18.4 - - + +
132D VAL 3.8 1.0 - - - +
133D GLN* 3.8 0.7 - - - -
134D ASP* 2.8 23.1 + - - +
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Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C ASP* 3.7 22.4 + - - +
147C THR* 5.0 3.9 + - - +
32D LYS* 1.3 76.9 - - - +
34D GLY* 1.3 61.7 + - - +
65D LYS 2.9 29.3 + - - -
66D GLY* 3.8 17.7 + - - +
67D VAL* 3.6 6.9 - - + +
68D GLN* 2.9 29.3 + - - +
69D VAL 3.9 1.0 + - - -
131D VAL* 4.3 15.0 - - + -
132D VAL 3.5 7.9 - - - +
133D GLN* 4.3 22.3 - - + +
161D LEU* 4.1 34.7 + - + +
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Residues in contact with GLY 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PHE* 3.9 17.1 - - - -
32D LYS 4.0 0.2 - - - -
33D LYS* 1.3 77.5 - - - +
35D VAL* 1.3 63.4 + - - +
67D VAL* 4.0 2.9 - - - -
69D VAL* 3.2 14.8 - - - -
131D VAL* 3.5 8.3 - - - +
132D VAL 2.8 36.5 + - - +
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Residues in contact with VAL 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D PHE* 3.6 9.1 - - - -
34D GLY* 1.3 79.2 - - - +
36D LEU* 1.3 70.2 + - - +
37D PHE* 4.5 1.3 - - + +
55D PHE* 3.9 26.7 - - + -
62D LEU* 4.7 5.2 - - + -
67D VAL* 4.0 22.0 - - + -
69D VAL 3.0 5.3 + - - -
70D VAL* 3.3 15.5 - - + -
71D ALA 2.9 26.5 + - - -
129D SER* 5.1 0.2 - - - -
130D MET 3.3 13.2 - - - +
131D VAL* 4.9 3.8 - - + -
157D ILE* 4.1 27.6 - - + -
161D LEU* 5.0 0.7 - - + -
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Residues in contact with LEU 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.8 16.2 - - + -
25D LEU* 4.5 14.6 - - + -
29D PHE* 3.8 18.5 - - + -
35D VAL* 1.3 74.1 - - - +
37D PHE* 1.3 59.9 + - - +
71D ALA* 3.4 26.0 - - + +
72D CYS 5.0 0.2 - - - -
73D LEU* 4.1 21.3 - - + -
97D LEU* 5.0 0.7 - - + -
104D PHE* 3.7 36.1 - - + -
128D PHE* 3.8 14.6 - - + -
129D SER* 3.4 1.4 - - - -
130D MET* 2.8 36.4 + - - +
132D VAL* 4.4 9.1 - - + +
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Residues in contact with PHE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D VAL* 4.6 0.9 - - + -
36D LEU* 1.3 75.7 - - - +
38D GLY* 1.3 50.4 - - - +
39D VAL* 4.1 9.9 - - + -
51D HIS* 3.6 24.9 - + - +
52D LEU* 4.0 23.6 - - + -
55D PHE* 3.4 52.0 - + + -
70D VAL* 4.0 13.7 - - + -
71D ALA 2.8 17.7 + - - +
72D CYS* 3.2 38.1 - - + -
73D LEU* 2.8 33.1 + - - +
94D VAL* 4.0 3.6 - - + -
128D PHE* 3.2 18.8 - - - +
129D SER* 4.0 11.7 - - - -
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Residues in contact with GLY 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 1.3 74.5 - - - +
39D VAL* 1.3 62.0 + - - -
51D HIS* 3.5 11.4 - - - -
73D LEU* 3.3 9.6 - - - -
125D LEU* 4.5 2.7 - - - -
126D LYS 4.2 4.3 - - - -
127D ARG* 3.4 4.9 - - - -
128D PHE* 2.9 52.0 + - - -
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Residues in contact with VAL 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D PHE* 4.1 6.1 - - + -
38D GLY* 1.3 78.3 - - - -
40D PRO* 1.3 69.1 - - - +
41D GLY 3.9 7.4 - - - +
47D CYS* 3.5 17.0 - - + +
51D HIS* 3.5 24.2 - - + +
72D CYS* 3.8 18.8 - - - -
73D LEU 3.0 9.1 + - - +
74D SER* 3.5 31.8 - - - -
84D TRP* 3.9 24.9 - - + -
125D LEU* 3.9 11.9 + - - +
127D ARG* 4.0 3.4 - - - +
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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