Contacts of the strand formed by residues 11 - 17 (chain E) in PDB entry 5HMG
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 ALA 11 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E THR* 1.3 74.6 - - - +
12E THR* 1.3 65.8 + - - +
27F GLN 3.6 11.2 - - - +
28F ASN* 4.1 12.3 - - + +
139F LYS* 3.7 6.6 - - - +
140F ILE* 2.8 39.7 + - + +
144F CYS* 3.8 29.4 - - + +
149F ILE* 4.8 3.6 - - + -
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Residues in contact with THR 12 (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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11E ALA* 1.3 78.7 + - - +
13E LEU* 1.3 63.4 + - - +
14E CYS* 4.0 21.9 - - - -
26F HIS* 3.0 9.8 - - - +
27F GLN* 2.8 48.8 + - - +
133F MET* 4.1 19.0 - - + +
137F CYS* 4.1 7.2 - - + -
138F PHE 3.4 10.5 - - - +
139F LYS* 5.4 0.7 - - - +
140F ILE* 5.0 1.3 - - - -
149F ILE* 5.4 0.4 - - - -
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Residues in contact with LEU 13 (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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12E THR* 1.3 73.2 - - - +
14E CYS* 1.3 61.7 + - - +
15E LEU* 5.4 0.4 - - + -
24F PHE* 3.8 34.1 - - + -
25F ARG 3.5 13.0 - - - +
26F HIS* 4.1 11.0 - - + -
122F THR* 4.0 19.1 - - + -
126F LEU* 5.1 1.3 - - + -
136F GLY 4.1 0.2 - - - +
137F CYS* 3.0 3.1 - - - +
138F PHE* 2.7 43.4 + - + +
140F ILE* 4.3 11.1 - - + +
149F ILE* 4.2 23.8 - - + -
152F ILE* 3.9 34.3 - - + -
153F ARG* 5.3 1.3 - - + -
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Residues in contact with CYS 14 (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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12E THR* 4.0 11.4 - - - -
13E LEU* 1.3 77.0 - - - +
15E LEU* 1.3 67.2 + - - +
14F TRP* 3.6 8.1 - - + -
24F PHE* 3.4 6.1 - - - +
25F ARG* 2.7 45.2 + - + +
136F GLY 3.5 3.8 - - - +
137F CYS* 2.0 47.8 - - - -
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Residues in contact with LEU 15 (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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13E LEU* 5.2 1.1 - - + +
14E CYS* 1.3 78.7 - - - +
16E GLY* 1.3 60.1 + - - +
10F ILE* 3.9 16.0 - - + +
14F TRP* 3.8 7.0 - - - -
23F GLY 3.4 3.1 - - - -
24F PHE* 3.8 16.8 - - + -
115F MET* 3.8 9.9 - - + -
118F LEU* 3.7 57.7 - - + +
119F PHE* 3.8 17.3 - - + +
122F THR* 4.0 9.2 - - + +
135F ASN 5.1 1.0 - - - +
136F GLY* 2.8 18.4 + - - +
138F PHE* 3.6 33.4 - - + -
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Residues in contact with GLY 16 (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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15E LEU* 1.3 77.4 - - - +
17E HIS* 1.3 60.8 + - - -
10F ILE* 4.1 14.8 - - - -
14F TRP* 3.6 20.1 - - - -
22F TYR* 3.4 3.5 - - - -
23F GLY 2.9 30.9 + - - +
115F MET* 3.6 12.1 - - - +
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Residues in contact with HIS 17 (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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16E GLY* 1.3 74.1 - - - +
18E HIS* 1.3 73.0 + - - +
320E MET* 3.5 23.0 - - + -
321E ARG 4.7 2.7 - - - -
323E VAL* 4.4 10.8 - - + -
6F ILE* 3.5 41.4 - - + +
7F ALA 4.5 0.2 + - - -
10F ILE* 3.8 26.5 + - + +
12F ASN 3.9 4.1 + - - -
13F GLY* 3.2 23.5 - - - -
14F TRP* 3.0 25.1 + - - -
17F MET* 5.0 2.5 - - - -
21F TRP 3.0 14.1 - - - +
22F TYR* 4.0 10.8 - - + +
115F MET* 3.9 5.6 - - - -
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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