Contacts of the helix formed by residues 127 - 131 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106G ASN* 4.0 0.2 - - - -
125G PRO* 4.8 3.6 + - + +
126G VAL* 1.3 73.4 - - - +
128G TYR* 1.3 64.4 + - - +
129G ALA 3.6 0.7 + - - -
130G GLY* 3.5 9.7 + - - -
131G VAL 3.5 11.0 - - - +
132G ALA* 3.4 6.1 - - - -
133G CYS* 3.3 25.5 + - - -
135G MSE 3.7 25.4 - - + -
151G GLU* 2.5 41.0 + - + +
152G ASP 3.8 7.5 + - - +
153G ALA* 3.9 23.6 - - + -
155G GLN* 4.0 13.2 + - - +
156G GLY* 4.4 7.4 + - - -
166G LEU* 3.4 30.7 - - + +
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Residues in contact with TYR 128 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G TYR* 3.1 36.8 + + - -
104G THR 3.9 8.6 - - - +
105G MSE 3.6 34.8 - - + +
106G ASN* 3.0 21.3 + - - +
126G VAL* 3.1 11.3 + - + +
127G HIS* 1.3 65.9 - - - +
129G ALA* 1.3 69.3 + - + +
130G GLY 3.0 4.5 - - - -
131G VAL* 2.8 31.7 + - - +
155G GLN* 3.9 5.8 - - - -
292G MSE 3.9 17.1 - - - -
294G TYR* 4.3 12.6 - + - -
320G HIS* 2.6 38.6 + + - -
321G TYR* 3.5 17.0 - - - -
350G LEU* 3.4 13.6 - - + +
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Residues in contact with ALA 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128G TYR* 1.3 87.8 - - + +
130G GLY* 1.3 58.5 + - - +
131G VAL* 3.1 13.5 + - + +
155G GLN* 2.7 20.9 + - - -
288G GLN* 4.2 8.9 - - - +
289G ASN* 3.9 4.5 - - - +
291G HIS* 4.1 14.4 + - - -
292G MSE 3.6 32.1 + - + +
294G TYR* 4.3 15.5 - - + -
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Residues in contact with GLY 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127G HIS 3.5 8.5 + - - -
128G TYR 3.0 2.0 - - - -
129G ALA* 1.3 77.1 - - - +
131G VAL* 1.3 59.9 - - - +
132G ALA 3.8 2.1 + - - -
155G GLN* 3.4 18.9 + - - +
156G GLY* 4.1 4.0 - - - -
159G SER* 3.3 24.4 + - - -
166G LEU* 4.7 1.8 - - - -
287G VAL 4.3 1.0 - - - +
288G GLN* 3.6 10.9 - - - -
289G ASN* 3.2 18.6 - - - -
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Residues in contact with VAL 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G THR* 4.3 5.8 - - + +
106G ASN* 3.2 20.0 + - - +
127G HIS* 3.5 15.7 + - - -
128G TYR 2.8 14.8 + - - +
129G ALA* 3.9 13.9 - - + +
130G GLY* 1.3 79.9 - - - +
132G ALA* 1.3 69.8 + - - +
280G PRO* 6.3 2.5 - - + -
281G SER 4.3 11.7 - - - +
282G ILE* 4.7 10.3 - - + -
283G PRO* 3.7 29.6 - - + -
286G CYS* 4.8 5.6 - - + -
288G GLN* 4.5 18.6 - - + +
294G TYR* 6.1 2.5 - - + +
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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