Contacts of the helix formed by residues 137 - 141 (chain B) in PDB entry 5E2B
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 VAL 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68B CYS 3.8 15.9 - - - +
69B GLY* 4.1 5.2 - - - -
119B LEU* 3.9 17.2 - - + +
134B ILE* 3.6 26.7 - - + -
135B GLN 3.9 5.8 - - - +
136B TRP* 1.3 78.9 - - - +
138B ILE* 1.3 69.9 + - - +
139B GLY 3.1 3.4 - - - -
140B HIS* 2.9 21.8 + - + +
141B LEU* 4.2 4.4 + - + +
167B ASP* 2.9 1.8 + - - -
301B SAH 3.5 51.1 - - + +
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Residues in contact with ILE 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 6.0 1.3 - - + -
134B ILE* 3.7 26.2 - - + +
137B VAL* 1.3 77.5 - - - +
139B GLY* 1.3 59.6 + - - +
140B HIS 3.0 4.8 + - - -
141B LEU* 3.2 17.3 + - - +
146B LEU* 3.9 37.6 - - + +
165B ILE* 4.0 31.4 - - + -
167B ASP* 3.0 26.6 + - + +
168B ASN 5.4 1.6 - - - +
169B MET* 4.4 4.3 - - + -
185B ARG* 2.9 22.1 + - + +
190B VAL* 4.3 25.4 - - + -
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Residues in contact with GLY 139 (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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12B PHE* 3.4 9.5 - - - -
137B VAL 3.0 1.8 + - - -
138B ILE* 1.3 81.0 - - - +
140B HIS* 1.3 55.1 + - - +
141B LEU 3.3 2.0 - - - -
167B ASP* 4.3 3.8 + - - -
182B SER* 3.3 9.3 - - - -
183B VAL* 2.8 50.7 + - - +
185B ARG* 3.8 7.6 - - - -
101E UNX 4.4 7.0 - - - -
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Residues in contact with HIS 140 (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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12B PHE* 3.2 10.2 - - - -
13B TYR* 3.0 25.5 - - - -
16B ALA* 3.4 17.2 - - + +
20B TRP* 3.0 27.0 + + - -
136B TRP 5.2 2.7 - - - -
137B VAL* 2.9 23.8 + - + +
139B GLY* 1.3 76.2 - - - +
141B LEU* 1.3 60.8 + - + +
180B ASP* 3.2 32.2 + - - -
181B SER 3.0 18.6 + - - -
182B SER* 3.7 14.1 - - - -
301B SAH 3.5 37.6 + + + +
1E 3BY 5.8 1.7 - - - -
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Residues in contact with LEU 141 (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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2B THR* 4.3 2.4 - - - +
12B PHE* 4.1 4.7 - - - -
13B TYR* 3.6 10.8 - - + +
119B LEU* 4.1 25.4 - - + -
120B GLN* 3.9 13.9 - - + +
137B VAL 4.7 3.4 - - - +
138B ILE* 3.2 12.4 + - - +
139B GLY 4.3 3.8 - - - +
140B HIS* 1.3 89.4 - - + +
142B THR* 1.3 59.8 + - - +
145B HIS* 3.8 25.4 - - + +
146B LEU* 3.9 18.4 - - + +
149B PHE* 4.1 15.5 - - + -
185B ARG* 2.7 28.2 + - - -
301B SAH 3.8 21.1 - - + +
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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