Contacts of the helix formed by residues 351 - 356 (chain A) in PDB entry 1P8Z
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 THR 351 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A LEU* 2.9 9.7 - - - +
350A SER* 1.3 80.2 - - - +
352A PHE* 1.3 61.7 + - - +
353A GLN 3.0 7.0 + - - -
354A GLN* 3.1 21.8 + - - +
355A MET* 4.1 6.2 + - - +
27G VAL* 4.3 22.6 - - + +
29G HIS* 4.5 8.1 - - + -
32G PHE* 4.1 17.0 - - + -
51G LEU* 6.0 0.2 - - + -
104G PHE* 3.5 20.2 - - + -
107G GLN* 2.4 41.5 + - - +
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Residues in contact with PHE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A LEU* 4.4 7.4 - - + -
133A TYR* 3.3 50.9 - + + -
346A LEU* 3.4 35.9 - - + +
347A ALA* 3.4 21.1 - - + +
349A LEU* 2.8 14.0 + - + +
351A THR* 1.3 79.0 + - - +
353A GLN* 1.3 64.5 + - - +
354A GLN 3.2 1.0 + - - -
355A MET* 3.2 31.5 + - + +
356A TRP* 3.1 66.6 + + - +
107G GLN* 5.8 0.2 - - - +
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Residues in contact with GLN 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A LEU 4.2 1.6 + - - -
350A SER 3.8 16.5 + - - +
351A THR 3.0 0.6 + - - +
352A PHE* 1.3 77.4 - - - +
354A GLN* 1.3 69.0 + - - +
356A TRP* 3.2 29.2 + - + +
28G GLU* 3.8 18.7 - - - +
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Residues in contact with GLN 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350A SER 4.7 3.3 - - - +
351A THR 3.1 16.7 - - - +
353A GLN* 1.3 87.4 - - - +
355A MET* 1.3 60.7 + - + +
356A TRP 3.2 10.3 + - - +
26G VAL* 3.5 20.4 + - - +
27G VAL* 3.0 31.4 - - + +
28G GLU* 2.7 48.6 + - - +
29G HIS* 3.8 3.6 + - - +
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Residues in contact with MET 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A TYR* 3.1 35.2 - - + +
346A LEU* 4.8 6.7 - - + -
351A THR* 4.4 7.4 - - - +
352A PHE* 3.2 36.7 + - + +
354A GLN* 1.3 77.8 - - + +
356A TRP* 1.3 67.0 + - - +
357A ILE* 4.5 4.3 - - - +
26G VAL 5.1 9.4 - - - +
27G VAL* 5.5 4.7 - - + -
107G GLN* 2.9 39.3 - - + +
110G ASP* 6.1 1.3 - - - +
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Residues in contact with TRP 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ALA* 3.8 22.0 - - + -
102A PRO* 3.3 32.7 - - + +
103A THR 3.5 31.6 - - - -
104A LEU 4.0 2.5 - - - -
131A ALA* 3.8 17.3 - - + -
132A MET* 3.5 28.3 - - - -
133A TYR* 3.9 3.6 - - + -
347A ALA* 4.4 4.5 - - + -
352A PHE* 3.1 51.2 + + - +
353A GLN* 3.2 31.7 - - + +
354A GLN 3.2 9.4 - - - +
355A MET* 1.3 83.6 - - - +
357A ILE* 1.3 69.2 + - - +
358A THR* 4.1 5.4 - - + +
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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