Contacts of the strand formed by residues 129 - 133 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126B LEU* 2.9 12.4 + - + +
128B GLU* 1.3 90.8 + - - +
130B ALA* 1.3 61.0 + - + +
140B ILE* 3.7 3.5 - - + +
141B TYR* 2.8 31.9 + - - +
142B HIS* 3.9 4.3 - - + -
157B TYR* 2.8 28.5 + - - +
159B HIS* 2.9 31.2 + - - +
162B TYR* 3.7 11.1 - - - +
163B ARG* 3.7 16.0 - - - +
166B ALA* 3.7 22.2 - - + +
167B LEU* 5.7 0.2 - - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 3.6 39.2 + - + -
127B ARG 4.1 8.3 - - - +
128B GLU 3.4 2.9 + - - +
129B ASN* 1.3 81.4 + - - +
131B GLU* 1.3 68.6 + - - +
138B PHE* 4.3 8.1 - - + -
139B LYS 3.1 18.8 - - - +
140B ILE* 4.1 3.8 - - + -
141B TYR* 4.2 1.8 - - - -
170B ARG* 4.6 4.4 + - - -
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Residues in contact with GLU 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA* 1.3 73.9 - - - +
132B GLU* 1.3 62.2 + - - +
133B MET* 4.2 0.2 - - - +
138B PHE* 3.3 6.0 - - - -
139B LYS* 2.8 32.6 + - - +
141B TYR* 3.5 17.0 + - + -
170B ARG* 2.8 36.5 + - - +
127D ARG* 2.6 43.1 + - - +
128D GLU* 3.3 21.9 - - - +
163D ARG* 2.6 34.7 + - - -
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PHE* 4.6 1.7 - - - -
119B PHE* 3.4 35.2 - - + -
123B ARG* 5.4 2.8 - - + -
131B GLU* 1.3 72.0 - - - +
133B MET* 1.3 58.9 + - - +
134B GLY* 3.1 20.9 + - - +
136B GLY 4.5 1.1 + - - +
137B CYS 3.9 4.9 - - - +
138B PHE* 4.0 12.9 - - + -
123D ARG* 3.0 18.7 + - - +
124D ARG* 2.7 48.5 + - + +
127D ARG* 3.5 24.3 - - - +
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Residues in contact with MET 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 4.0 17.7 - - + +
131B GLU 4.2 0.7 - - - +
132B GLU* 1.3 73.2 - - - +
134B GLY* 1.3 58.5 + - - +
135B ASN* 3.1 20.8 + - - +
137B CYS* 2.9 40.2 + - - +
138B PHE 4.0 0.9 - - - -
139B LYS* 3.5 44.0 - - + +
124D ARG 5.6 2.5 - - - -
127D ARG* 4.5 19.5 - - - +
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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