Contacts of the strand formed by residues 133 - 136 (chain E) in PDB entry 4HHM
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 133 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87E PRO 3.5 12.2 + - - +
88E MET* 3.2 11.7 - - + +
89E ALA 3.1 22.5 + - - -
131E ALA* 3.5 3.7 - - - +
132E LYS* 1.3 86.9 - - + +
134E TYR* 1.3 63.4 + - - +
135E VAL* 4.4 0.7 - - + -
176E ILE* 5.4 0.7 - - - -
177E ARG* 3.6 30.7 - - - +
179E ALA* 4.2 13.5 - - + -
242E PHE* 4.2 11.7 - - + +
243E HIS* 3.8 35.4 - - + -
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Residues in contact with TYR 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E ALA* 3.2 17.9 - - + -
90E THR* 3.7 3.8 - - - -
91E THR* 2.3 34.8 + - - -
119E THR* 3.7 13.2 + - + -
122E ASN* 2.9 52.8 + - - +
123E ILE* 3.9 18.6 - - + -
126E ALA* 4.0 15.7 - - + -
132E LYS 4.3 0.2 - - - -
133E VAL* 1.3 73.2 - - - +
135E VAL* 1.3 77.2 + - - +
136E ALA* 3.9 2.4 + - + -
176E ILE* 5.0 9.6 - - + -
177E ARG 2.9 11.4 + - - +
178E PHE* 3.3 35.5 - + + +
179E ALA 3.0 20.8 + - - -
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Residues in contact with VAL 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E MET* 3.5 40.8 - - + -
89E ALA 3.0 5.9 + - - -
90E THR* 2.6 35.4 + - + +
91E THR 4.0 0.7 + - - -
133E VAL* 4.4 0.2 - - + -
134E TYR* 1.3 83.1 - - - +
136E ALA* 1.3 67.6 + - - +
137E TRP* 4.4 2.5 - - + +
179E ALA* 3.4 23.6 - - + +
181E GLU* 3.7 23.1 - - + +
215E ASN* 3.9 15.5 - - - +
243E HIS* 4.2 4.7 - - + -
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Residues in contact with ALA 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E THR* 4.5 0.4 - - - -
104E PHE* 5.3 5.8 - - + -
134E TYR* 3.9 4.7 + - + +
135E VAL* 1.3 75.4 - - - +
137E TRP* 1.3 60.4 + - - +
138E GLY 4.0 1.4 + - - -
162E PHE* 3.7 36.3 - - + -
165E LEU* 6.0 1.6 - - + -
178E PHE* 5.6 4.5 - - + -
179E ALA 3.0 10.8 + - - +
180E ILE* 3.5 6.4 - - + +
181E GLU 2.8 27.5 + - - -
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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