Contacts of the helix formed by residues 139 - 143 (chain B) in PDB entry 1PTH
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 TRP 139 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225A GLY* 5.1 12.2 - - - -
227A GLY 6.2 0.4 - - - -
228A VAL 4.4 1.6 - - - -
229A ASP* 3.4 32.4 + - + +
330A GLN* 3.7 1.6 + - - +
333A ARG* 4.0 41.9 - - - +
334A LEU* 3.3 18.0 - - + +
337A ILE* 3.8 19.5 - - + -
537A ASN* 3.7 20.6 - - - -
538A PRO* 3.3 43.1 - - + -
539A ILE* 4.8 5.8 - - + -
544A TYR* 6.0 1.8 - + - -
138B SER* 1.3 70.2 - - - +
140B GLU* 1.3 53.4 + - - +
142B PHE* 2.8 39.4 + + + +
143B SER* 2.6 47.5 + - - -
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Residues in contact with GLU 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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238A LEU* 4.1 18.5 - - + +
241A GLN* 5.7 3.1 - - - +
326A GLU* 5.9 0.7 - - - +
330A GLN* 3.8 20.5 + - - +
333A ARG* 5.7 3.5 - - - +
134B HIS* 3.8 15.0 - - + -
138B SER* 3.1 6.6 + - - +
139B TRP* 1.3 80.8 - - - +
141B SER* 1.3 57.4 + - - +
143B SER* 4.0 6.3 - - - -
144B ASN* 2.8 66.1 + - + +
147B TYR* 3.7 8.2 + - + +
1D NAG 3.3 25.0 + - - +
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Residues in contact with SER 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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128B PRO* 5.4 3.6 - - - +
129B THR 3.0 26.2 + - - -
130B TYR 3.8 2.3 - - - -
131B ASN* 3.7 40.1 - - - +
134B HIS* 4.1 1.3 - - - -
136B TYR 4.8 2.2 - - - -
138B SER* 2.8 28.2 + - - -
140B GLU* 1.3 75.4 - - - +
142B PHE* 1.3 60.9 + - - +
143B SER 3.5 0.3 + - - -
144B ASN 4.3 8.3 - - - +
147B TYR* 5.1 2.8 - - - +
149B THR* 5.9 0.5 - - - -
376B ARG* 3.3 13.0 + - - -
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Residues in contact with PHE 142 (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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373A TYR 5.1 0.9 - - - -
374A ARG* 6.1 0.2 - - - -
538A PRO* 3.4 43.1 - - + -
544A TYR* 3.4 31.0 - - + +
127B PRO* 3.9 12.8 - - + -
128B PRO* 4.3 7.6 - - + -
129B THR 5.3 0.2 + - - -
138B SER 3.3 6.6 + - - +
139B TRP* 2.8 37.1 + + + +
141B SER* 1.3 71.3 - - - +
143B SER* 1.3 61.0 + - - +
145B VAL* 4.9 1.0 - - - +
374B ARG* 3.6 34.1 - - - -
376B ARG* 2.6 27.3 + - - +
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Residues in contact with SER 143 (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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139B TRP* 2.6 48.4 + - - -
140B GLU* 4.0 5.1 - - - -
142B PHE* 1.3 81.2 - - - +
144B ASN* 1.3 61.0 + - - +
145B VAL* 3.0 18.4 + - - +
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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