Contacts of the helix formed by residues 132 - 137 (chain L) in PDB entry 3EXG
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 PHE 132 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J HIS* 6.1 0.2 - - - -
83L PHE* 3.8 17.0 - - + -
84L ASN* 3.7 26.7 - - - -
86L SER* 5.2 0.4 - - - -
87L MET* 3.7 28.0 - - + -
90L ILE* 5.5 0.4 - - + -
118L ASN* 3.0 25.7 + - - +
130L GLN* 3.4 52.3 - - + -
131L CYS* 1.3 73.5 - - - +
133L ALA* 1.3 65.9 + - - +
134L ALA* 3.4 2.9 - - - -
135L TRP* 3.2 28.6 + + + +
136L TYR* 3.2 49.4 + + + -
170L LEU* 4.2 4.0 - - + -
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Residues in contact with ALA 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131L CYS* 3.4 20.9 - - - -
132L PHE* 1.3 75.9 - - - +
134L ALA* 1.3 65.4 + - - +
136L TYR* 4.2 0.7 - - - +
137L GLY* 3.0 23.4 + - - -
144L VAL* 4.9 0.3 - - - +
170L LEU* 3.5 19.3 - - + +
212L HIS* 3.8 21.8 - - + -
241L ILE* 3.7 16.0 - - + +
271L VAL* 3.8 13.2 - - + -
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Residues in contact with ALA 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J HIS* 4.0 17.7 - - + +
269J PHE* 4.1 18.5 - - + +
131L CYS* 5.2 0.6 - - - +
132L PHE 5.0 0.4 - - - -
133L ALA* 1.3 80.3 - - - +
135L TRP* 1.3 68.4 + - + +
137L GLY 3.4 1.4 + - - -
138L HIS* 3.2 17.7 + - - +
269L PHE 3.5 24.9 - - - +
270L GLY* 3.8 14.8 - - - -
271L VAL* 4.0 5.4 - - - +
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Residues in contact with TRP 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J ILE* 3.8 29.4 - - + -
94J ILE* 4.1 15.3 - - + -
134J ALA 4.8 0.4 - - - -
135J TRP* 3.0 74.7 + + + +
136J TYR* 5.3 0.4 - - - -
138J HIS* 3.5 28.4 - + + +
139J CYS* 3.9 17.7 - - - -
87L MET* 4.2 12.8 - - + -
90L ILE* 4.1 19.1 - - + -
130L GLN* 4.2 10.8 - - - -
132L PHE* 3.2 41.1 + + + +
134L ALA* 1.3 80.4 - - + +
136L TYR* 1.3 61.2 - - + +
138L HIS* 2.9 23.0 - - - +
139L CYS* 4.1 0.5 - - - -
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Residues in contact with TYR 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135J TRP* 5.2 0.7 - + - -
83L PHE* 3.7 22.7 - + - -
86L SER* 2.9 27.1 + - - -
90L ILE* 3.4 41.5 - - + +
93L VAL* 4.2 18.6 - - + +
94L ILE* 4.8 4.7 - - + -
132L PHE* 3.2 45.5 + + + +
135L TRP* 1.3 74.6 - - + +
137L GLY* 1.3 59.9 + - - +
138L HIS 2.8 10.4 + - - -
139L CYS* 3.1 21.5 + - - +
142L LEU* 3.9 21.0 - - + +
144L VAL* 3.8 27.7 - - + +
168L VAL* 4.3 15.0 - - + -
170L LEU* 4.7 2.9 - - + -
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Residues in contact with GLY 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269J PHE* 3.1 22.0 - - - -
133L ALA 3.0 18.3 + - - -
134L ALA 3.9 0.2 - - - -
135L TRP 3.3 0.2 - - - -
136L TYR* 1.3 75.4 - - - +
138L HIS* 1.3 56.6 + - - +
139L CYS 3.4 0.7 - - - -
144L VAL* 3.8 15.1 - - - +
241L ILE* 3.9 14.4 - - - -
242L ARG* 3.1 28.2 + - - +
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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