Contacts of the helix formed by residues 126 - 130 (chain A) in PDB entry 1EQB
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 HIS 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A SER* 4.5 2.7 - - - -
119A MET 4.8 0.7 - - - +
121A LEU* 4.5 5.2 - - - +
124A GLY 4.0 0.4 + - - -
125A GLY* 1.3 75.1 - - - -
127A LEU* 1.3 65.1 + - + +
128A THR* 2.7 45.8 + - + -
129A HIS* 2.7 57.4 + - + +
131A SER 4.8 1.2 + - - -
175A SER* 3.0 22.6 + - - +
1291A PLP 3.4 44.9 - + + +
1293A FFO 3.0 39.2 + - - -
57B GLU* 4.9 2.0 + - - -
262B GLY* 5.7 2.2 - - - -
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A LEU* 3.6 20.6 - - + +
126A HIS* 1.3 87.8 - - + +
128A THR* 1.3 57.2 + - - +
129A HIS 3.0 4.9 + - - -
131A SER* 3.0 44.7 + - - +
133A VAL* 4.0 4.0 - - + -
134A ASN* 3.5 13.1 - - + +
136A SER* 3.2 3.8 + - - -
1293A FFO 2.9 59.3 + - + +
57B GLU* 4.8 1.1 - - - +
257B PHE* 4.0 11.2 - - + -
258B PRO* 3.9 28.5 - - + +
261B GLN 5.5 2.5 - - - +
262B GLY* 6.0 0.9 - - - -
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A SER* 3.9 22.0 - - - +
102A ASN* 2.7 33.1 + - - -
106A TYR* 2.5 33.6 + - - -
126A HIS* 2.7 28.0 + - + -
127A LEU* 1.3 75.7 - - + +
129A HIS* 1.3 54.0 + - - +
130A GLY 3.3 3.6 - - - -
134A ASN* 3.5 27.1 - - - +
135A PHE* 4.0 14.8 - - + -
136A SER* 3.5 1.6 - - - -
261B GLN 6.1 0.2 - - - +
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Residues in contact with HIS 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ASN* 4.4 3.1 - - - -
106A TYR* 3.8 6.5 - - - -
118A GLY* 3.9 18.7 - - - -
119A MET* 3.9 21.3 - - - +
125A GLY* 4.0 5.1 - - - -
126A HIS* 2.7 42.7 + - + +
128A THR* 1.3 92.2 - - - +
130A GLY* 1.3 55.9 + - - +
131A SER 3.8 0.9 - - - -
142A ILE* 4.4 5.1 - - - +
171A ILE* 4.0 27.3 - - + +
173A GLY* 3.9 28.5 + - - -
174A PHE 4.0 0.2 - - - -
198A PHE* 5.4 1.3 - + - -
200A ASP* 3.0 33.8 + - + +
1291A PLP 3.9 4.9 - - + -
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Residues in contact with GLY 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A THR 3.3 0.2 - - - -
129A HIS* 1.3 81.0 - - - +
131A SER* 1.3 65.9 + - - +
132A PRO* 3.3 5.2 - - - +
136A SER* 3.0 14.9 + - - -
137A GLY* 3.7 7.9 - - - -
142A ILE* 3.6 36.7 - - - +
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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