Contacts of the helix formed by residues 127 - 131 (chain H) in PDB entry 4PIW
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 127 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106H ASN* 4.1 0.4 - - - -
125H PRO* 4.5 3.3 + - - +
126H VAL* 1.3 71.9 - - - +
128H TYR* 1.3 62.7 + - - +
129H ALA 3.8 1.2 + - - -
130H GLY* 3.9 7.6 + - - -
131H VAL 3.5 12.1 - - - +
132H ALA* 3.4 20.8 - - + -
133H CYS* 3.4 16.9 + - - -
135H MSE 4.0 19.7 - - + -
151H GLU* 2.9 38.0 + - + +
152H ASP 3.7 12.5 + - - +
153H ALA* 3.9 31.0 - - + -
155H GLN* 4.0 15.8 + - - +
156H GLY* 4.9 1.3 - - - -
166H LEU* 3.5 24.7 - - + +
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Residues in contact with TYR 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79H TYR* 2.9 37.2 + + + +
104H THR 4.1 6.3 - - - +
105H MSE 3.7 22.2 - - + +
106H ASN* 3.0 21.6 + - - +
126H VAL* 3.2 9.2 + - + +
127H HIS* 1.3 69.2 - - - +
129H ALA* 1.3 70.1 + - + +
130H GLY 3.0 4.9 - - - -
131H VAL* 3.0 25.8 + - - +
155H GLN* 3.9 5.6 - - - -
292H MSE 3.3 31.0 - - + +
294H TYR* 4.4 5.8 - + - -
320H HIS* 2.8 39.7 + + - +
321H TYR* 3.5 23.8 - + - -
350H LEU* 3.4 12.9 - - + +
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Residues in contact with ALA 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H THR 5.9 0.2 - - - +
128H TYR* 1.3 87.8 - - + +
130H GLY* 1.3 55.0 + - - +
131H VAL* 3.1 13.1 + - + +
155H GLN* 2.8 18.7 + - - -
280H PRO* 6.2 0.2 - - + -
288H GLN* 3.8 18.1 - - - +
289H ASN* 4.1 2.9 - - - +
291H HIS* 4.3 11.5 + - - -
292H MSE 3.6 31.3 + - + +
294H TYR* 4.2 17.9 - - + -
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Residues in contact with GLY 130 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127H HIS* 3.9 5.8 + - - -
128H TYR 3.0 2.2 - - - -
129H ALA* 1.3 76.2 - - - +
131H VAL* 1.3 61.9 + - - +
132H ALA 3.5 2.4 + - - -
155H GLN* 3.4 20.2 + - - -
156H GLY* 4.2 1.8 - - - -
159H SER* 3.1 25.5 + - - -
166H LEU* 3.8 4.8 - - - +
287H VAL 4.4 0.7 - - - +
288H GLN* 4.0 8.0 - - - -
289H ASN* 3.3 20.2 - - - -
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Residues in contact with VAL 131 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104H THR* 4.4 6.1 - - + +
106H ASN* 3.5 18.9 + - - +
127H HIS* 3.5 14.3 - - - -
128H TYR 3.0 16.2 + - - +
129H ALA* 3.9 14.1 - - + +
130H GLY* 1.3 77.7 - - - +
132H ALA* 1.3 70.3 + - - +
280H PRO* 6.1 2.9 - - + -
281H SER 4.1 13.7 - - - +
282H ILE* 4.5 13.0 - - + -
283H PRO* 3.7 29.8 - - + -
286H CYS* 4.6 6.1 - - + -
287H VAL 6.0 0.2 - - - -
288H GLN* 4.4 17.5 - - + +
294H TYR* 6.0 2.7 - - + +
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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
------------------------------------------------------------
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