Contacts of the strand formed by residues 129 - 133 (chain D) 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 ASN 129 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D LEU* 2.9 13.6 + - + +
128D GLU* 1.3 92.2 + - - +
130D ALA* 1.3 60.0 + - + +
140D ILE* 3.7 2.6 - - + +
141D TYR* 2.8 33.0 + - - +
142D HIS* 3.9 4.0 - - + -
157D TYR* 2.8 28.1 + - - +
159D HIS* 2.9 32.8 + - - +
162D TYR* 3.8 10.9 - - - +
163D ARG* 3.7 13.9 - - - +
166D ALA* 3.7 20.7 - - + +
167D LEU* 5.8 0.2 - - - +
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Residues in contact with ALA 130 (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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126D LEU* 3.6 38.1 + - + -
127D ARG 4.1 9.1 + - - +
128D GLU 3.3 3.0 - - - +
129D ASN* 1.3 82.0 + - - +
131D GLU* 1.3 67.9 + - - +
138D PHE* 4.3 8.6 - - + -
139D LYS 3.1 18.6 - - - +
140D ILE* 4.1 4.5 - - + -
141D TYR* 4.2 2.0 - - - -
170D ARG* 4.6 4.4 + - - -
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Residues in contact with GLU 131 (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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130D ALA* 1.3 74.1 - - - +
132D GLU* 1.3 62.9 + - - +
133D MET 3.5 0.2 + - - -
138D PHE* 3.3 6.5 - - - -
139D LYS* 2.8 33.1 + - + +
141D TYR* 3.6 17.6 + - + -
170D ARG* 2.9 35.2 + - - +
171D PHE* 4.6 0.2 - - - -
127F ARG* 2.6 42.2 + - - +
128F GLU* 3.4 22.5 - - - +
163F ARG* 2.6 33.3 + - - -
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Residues in contact with GLU 132 (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 PHE* 4.6 1.9 - - - -
119D PHE* 3.4 36.8 - - + -
123D ARG* 5.4 3.0 - - + -
131D GLU* 1.3 73.2 - - - +
133D MET* 1.3 58.6 + - - +
134D GLY* 3.1 20.5 + - - +
135D ASN 4.6 0.3 + - - -
136D GLY 4.6 1.3 + - - +
137D CYS 3.9 7.0 - - - +
138D PHE* 4.0 12.6 - - + -
123F ARG* 3.0 18.6 + - - +
124F ARG* 2.8 45.6 + - + +
127F ARG* 3.5 21.9 - - - +
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Residues in contact with MET 133 (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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12C THR* 4.4 16.4 - - + +
131D GLU 3.5 1.0 + - - -
132D GLU* 1.3 71.0 - - - +
134D GLY* 1.3 61.0 + - - +
135D ASN* 3.1 30.5 + - - +
137D CYS* 2.9 28.9 + - + +
138D PHE 3.7 3.6 - - - +
139D LYS* 3.4 46.4 - - + -
124F ARG 5.6 2.2 - - - -
127F ARG* 4.1 21.8 - - - +
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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