Contacts of the helix formed by residues 344 - 349 (chain A) in PDB entry 4PGF
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 LEU 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55A HIS* 4.2 10.3 - - + -
80A ASN* 4.4 14.9 - - - +
83A SER* 5.1 0.2 - - - -
298A ASN* 3.2 12.2 - - - +
299A ILE* 3.9 6.5 - - - -
300A GLY 3.5 23.1 + - - +
301A HIS* 3.6 16.9 + - - +
303A ASP 5.9 0.2 - - - +
340A ALA* 4.7 0.2 - - - +
343A ARG* 1.3 73.6 - - - +
345A VAL* 1.3 59.7 + - - +
346A ASN* 3.5 15.3 - - - +
347A LEU* 3.5 36.6 - - + -
348A GLY* 3.0 24.8 + - - +
501A NAD 4.0 7.9 - - - +
502A ADN 3.5 25.1 - - - +
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Residues in contact with VAL 345 (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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199A LEU* 3.8 30.1 - - + +
202A GLY* 3.7 13.3 - - - -
203A ILE* 4.5 1.1 - - + +
297A CYS* 3.9 15.0 - - + -
298A ASN 2.8 21.6 + - - +
299A ILE* 4.3 3.8 - - + +
339A LEU* 3.8 32.8 - - + -
340A ALA* 4.8 2.5 - - - -
343A ARG 3.2 4.0 + - - +
344A LEU* 1.3 70.5 - - - +
346A ASN* 1.3 68.6 + - - +
347A LEU 3.3 0.9 - - - -
348A GLY* 3.7 2.9 - - - +
349A CYS* 3.1 36.6 + - + +
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Residues in contact with ASN 346 (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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198A SER* 3.5 43.1 + - - +
202A GLY* 4.6 1.1 - - - -
299A ILE* 3.4 18.1 - - + +
344A LEU* 3.5 9.0 - - - +
345A VAL* 1.3 79.2 - - - +
347A LEU* 1.3 69.6 + - - +
350A ALA* 3.1 18.7 - - - +
352A GLY* 2.9 21.2 + - - -
353A HIS* 3.7 8.5 + - - -
501A NAD 2.8 44.6 + - - -
502A ADN 4.2 0.6 - - - -
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Residues in contact with LEU 347 (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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55A HIS* 3.4 36.6 - - + +
57A THR* 3.9 29.2 - - + -
82A PHE 3.7 5.1 - - - +
83A SER* 3.9 18.6 - - - +
85A GLN* 4.6 1.0 + - - +
103A LYS* 3.7 10.4 + - - -
344A LEU* 3.5 22.2 + - + -
346A ASN* 1.3 82.7 + - - +
348A GLY* 1.3 63.9 + - - +
350A ALA 2.8 17.8 - - - +
351A MET 3.9 2.5 - - - +
352A GLY* 3.4 26.0 - - - +
502A ADN 3.9 24.0 - - + +
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Residues in contact with GLY 348 (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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80A ASN* 5.8 0.4 - - - -
82A PHE* 4.2 20.8 - - - +
103A LYS* 3.2 23.9 + - - -
324A GLN* 4.1 11.4 - - - +
340A ALA* 4.5 10.1 - - - -
344A LEU* 3.0 20.6 + - - +
345A VAL 4.1 0.4 - - - -
346A ASN 3.5 0.4 - - - -
347A LEU* 1.3 79.3 - - - +
349A CYS* 1.3 61.5 + - - +
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Residues in contact with CYS 349 (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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103A LYS* 5.7 0.4 - - - -
202A GLY* 3.4 19.5 - - - +
205A ARG* 3.3 22.7 - - - +
206A ALA* 3.9 17.7 - - + +
323A PRO 5.4 0.2 - - - -
324A GLN* 3.9 27.8 - - - -
325A VAL* 5.0 0.9 - - - -
339A LEU* 4.4 1.6 - - - -
340A ALA* 4.1 13.0 - - - -
345A VAL* 3.1 26.6 + - - +
348A GLY* 1.3 78.5 - - - +
350A ALA* 1.3 62.7 - - - +
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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
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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