Contacts of the strand formed by residues 32 - 39 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28E LEU 4.1 16.7 + - - +
29E PHE 3.3 8.9 - - - +
30E LYS 3.1 17.4 - - - +
31E GLY* 1.3 80.7 - - - +
33E LYS* 1.3 64.3 + - - +
34E GLY 4.0 0.2 + - - -
68E GLN* 3.7 34.0 + - + +
69E VAL* 4.3 16.1 - - + +
132E VAL 3.8 1.4 - - - +
133E GLN* 3.8 2.0 - - - -
134E ASP* 2.8 27.8 + - - +
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Residues in contact with LYS 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LYS* 1.3 75.7 - - - +
34E GLY* 1.3 63.3 + - - +
65E LYS 3.2 27.2 + - - -
66E GLY* 3.8 16.6 - - - +
67E VAL* 3.5 5.0 - - + +
68E GLN* 2.9 33.3 + - - +
69E VAL* 3.7 2.9 + - - +
131E VAL* 4.5 6.7 - - + -
132E VAL 3.5 7.4 - - - +
133E GLN* 4.2 32.1 - - + +
161E LEU* 3.9 42.8 + - + +
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Residues in contact with GLY 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE* 3.8 8.2 - - - -
32E LYS 4.0 0.8 + - - -
33E LYS* 1.3 77.4 - - - +
35E VAL* 1.3 64.2 + - - +
67E VAL* 3.9 2.9 - - - -
69E VAL* 3.1 23.1 - - - -
131E VAL* 3.6 7.1 - - - +
132E VAL 2.7 37.4 + - - +
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Residues in contact with VAL 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E PHE* 3.6 6.9 - - - -
34E GLY* 1.3 79.0 - - - +
36E LEU* 1.3 70.8 + - - +
37E PHE* 4.6 1.8 - - + +
55E PHE* 3.8 29.4 - - + -
62E LEU* 4.4 13.9 - - + -
67E VAL* 4.1 22.9 - - + -
69E VAL 2.9 9.2 + - - +
70E VAL* 3.3 12.3 - - + -
71E ALA 2.9 26.0 + - - -
130E MET 3.3 12.6 - - - +
131E VAL* 4.8 3.1 - - + -
157E ILE* 4.0 18.4 - - + -
161E LEU* 4.6 4.3 - - + -
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Residues in contact with LEU 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 3.9 19.7 - - + -
25E LEU* 4.2 12.1 - - + -
29E PHE* 3.9 15.2 - - + -
35E VAL* 1.3 76.9 - - - +
37E PHE* 1.3 64.5 + - - +
71E ALA* 3.4 28.5 - - + +
73E LEU* 4.3 13.9 - - + -
97E LEU* 4.9 0.7 - - + -
104E PHE* 3.7 34.5 - - + -
128E PHE* 3.8 8.7 - - + -
129E SER* 3.3 1.7 - - - -
130E MET* 2.7 55.7 + - + +
132E VAL* 4.5 3.3 - - + +
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Residues in contact with PHE 37 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E VAL* 4.7 0.4 - - + -
36E LEU* 1.3 76.3 - - - +
38E GLY* 1.3 51.1 + - - +
39E VAL* 4.0 11.0 - - + -
51E HIS* 3.6 22.2 - + - +
52E LEU* 4.0 24.9 - - + -
55E PHE* 3.3 53.8 - + + -
70E VAL* 4.0 7.2 - - + -
71E ALA 2.8 16.8 + - - +
72E CYS* 3.2 37.7 - - + -
73E LEU* 2.8 33.3 + - - +
94E VAL* 4.0 8.3 - - + -
128E PHE* 3.2 18.4 - - - +
129E SER* 4.0 11.9 - - - -
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Residues in contact with GLY 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E PHE* 1.3 72.1 - - - +
39E VAL* 1.3 66.9 + - - +
51E HIS* 3.6 5.4 - - - -
73E LEU* 3.3 9.4 - - - -
125E LEU* 4.5 2.9 - - - -
126E LYS 4.2 6.3 - - - -
127E ARG* 3.4 5.0 - - - -
128E PHE* 2.9 52.4 + - - +
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Residues in contact with VAL 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E PHE* 4.0 7.2 - - + -
38E GLY* 1.3 74.0 - - - -
40E PRO* 1.3 66.7 - - - +
41E GLY 4.0 6.7 - - - +
47E CYS* 3.6 16.8 - - + -
51E HIS* 3.4 28.5 - - + +
52E LEU 5.3 0.2 - - - +
72E CYS* 3.8 25.4 - - - -
73E LEU 3.0 10.2 + - - +
74E SER* 3.6 32.6 - - - -
75E VAL 4.5 0.5 + - - -
84E TRP* 3.9 18.2 - - + -
125E LEU* 4.0 10.5 - - - +
127E ARG* 4.1 2.2 - - - +
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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