Contacts of the helix formed by residues 126 - 130 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A GLU* 4.9 2.0 + - - -
262A GLY* 5.8 1.9 - - - -
99B SER* 4.4 3.4 - - - -
119B MET 4.7 0.9 - - - +
121B LEU* 4.5 5.3 + - - +
124B GLY 4.0 0.4 + - - -
125B GLY* 1.3 75.7 - - - -
127B LEU* 1.3 64.5 + - + +
128B THR* 2.7 46.7 + - + -
129B HIS* 2.8 55.8 + - + +
130B GLY 4.3 0.2 + - - -
131B SER 4.8 1.0 + - - -
175B SER* 3.1 22.2 + - - +
2291B PLP 3.4 43.4 + + + +
2293B FFO 3.0 38.0 + - - -
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Residues in contact with LEU 127 (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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57A GLU* 4.8 0.9 - - - +
257A PHE* 4.1 10.5 - - + -
258A PRO* 4.0 23.1 - - + +
261A GLN 5.6 2.2 - - - +
262A GLY* 6.0 1.1 - - - -
121B LEU* 3.6 20.2 - - + +
126B HIS* 1.3 87.7 - - + +
128B THR* 1.3 57.4 + - + +
129B HIS 3.1 0.2 + - - -
131B SER* 3.0 48.3 + - - +
133B VAL* 4.0 4.5 - - + -
134B ASN* 3.5 13.5 - - + +
136B SER* 3.2 4.3 + - - -
2293B FFO 3.0 64.0 + - + +
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Residues in contact with THR 128 (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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99B SER* 3.9 22.0 - - - +
102B ASN* 2.7 32.9 + - - -
106B TYR* 2.4 33.4 + - - -
126B HIS* 2.7 28.7 + - + -
127B LEU* 1.3 74.1 - - - +
129B HIS* 1.3 54.2 + - - +
130B GLY 3.3 3.4 - - - -
134B ASN* 3.5 27.6 - - - +
135B PHE* 4.1 14.8 - - + -
136B SER* 3.5 2.4 - - - -
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Residues in contact with HIS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ASN* 4.4 3.1 - - - -
106B TYR* 3.8 6.7 - - - -
118B GLY* 3.9 19.2 - - - -
119B MET* 4.0 20.6 - - - +
125B GLY* 4.0 5.1 - - - -
126B HIS* 2.8 43.9 + - + +
128B THR* 1.3 92.1 - - - +
130B GLY* 1.3 57.3 + - - +
131B SER 3.8 0.4 - - - -
142B ILE* 4.4 4.7 - - - +
171B ILE* 4.0 26.6 - - + +
173B GLY* 3.9 24.1 + - - -
174B PHE 4.0 0.2 - - - -
198B PHE* 5.4 1.3 - + - -
200B ASP* 3.0 35.3 + - + +
2291B PLP 3.9 8.3 - - + -
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Residues in contact with GLY 130 (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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128B THR 3.3 0.2 - - - -
129B HIS* 1.3 81.1 - - - +
131B SER* 1.3 65.2 - - - +
132B PRO* 3.3 5.4 - - - +
136B SER* 3.0 15.3 + - - -
137B GLY* 3.8 7.8 - - - -
142B ILE* 3.6 36.5 - - - +
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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