Contacts of the helix formed by residues 317 - 323 (chain B) in PDB entry 1PG4
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 317 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 4.4 14.4 - - + -
146B ALA* 3.7 36.1 - - + +
149B MET* 3.8 34.5 - - + -
150B LEU* 5.6 2.0 - - + -
307B VAL* 4.2 9.4 - - + -
312B GLY 3.2 6.6 + - - +
313B HIS* 3.9 6.3 - - - +
316B LEU* 1.3 102.0 - - + +
318B TYR* 1.3 73.0 + - + +
319B GLY 3.5 1.8 - - - -
320B PRO* 3.4 2.2 - - - +
321B LEU* 2.9 48.3 + - + +
327B THR* 4.8 1.8 - - + -
329B MET* 4.7 3.6 - - + -
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Residues in contact with TYR 318 (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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77B LEU* 3.5 38.8 - - + -
81B CYS* 3.8 8.9 - - - -
149B MET* 3.5 32.0 + - + +
150B LEU* 3.9 17.0 - - + -
153B ALA* 4.5 2.8 - - + +
159B HIS* 2.8 38.7 + + - -
259B LEU* 4.7 0.7 - - + -
260B PHE* 4.4 10.3 - + - -
281B TYR* 3.7 28.3 - + + +
282B LEU* 4.0 15.6 - - + +
285B ALA* 5.0 1.1 - - + -
313B HIS* 3.0 22.3 + - + +
317B LEU* 1.3 85.7 - - + +
319B GLY* 1.3 62.3 + - - +
322B ALA* 3.0 27.5 + - - +
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Residues in contact with GLY 319 (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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285B ALA* 3.7 27.7 - - - +
286B ALA* 4.1 2.1 - - - -
289B PHE* 4.0 7.4 - - - -
314B SER 2.9 21.3 + - - -
318B TYR* 1.3 76.3 - - - +
320B PRO* 1.3 65.8 - - - +
322B ALA* 3.4 2.1 + - - +
323B CYS* 3.2 26.0 + - - -
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Residues in contact with PRO 320 (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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289B PHE* 3.7 35.0 - - + -
301B TYR* 4.3 2.5 - - + -
314B SER 3.6 9.0 - - - +
315B TYR* 3.8 15.3 - - - +
316B LEU 3.2 29.6 - - - +
317B LEU 3.4 5.8 - - - +
319B GLY* 1.3 90.0 - - - +
321B LEU* 1.3 58.7 + - - +
323B CYS 3.1 3.1 + - - -
324B GLY 3.1 4.2 + - - -
325B ALA* 2.9 32.5 + - + +
327B THR* 4.0 16.6 - - - +
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Residues in contact with LEU 321 (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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81B CYS* 3.5 21.3 - - + +
85B HIS* 2.8 27.9 + - - -
94B ALA* 4.0 24.7 - - + +
95B ILE* 4.7 1.3 - - + -
110B TYR* 3.3 28.4 + - + +
113B LEU* 4.1 9.9 - - + -
150B LEU* 4.0 32.1 - - + -
317B LEU* 2.9 42.8 + - + +
320B PRO* 1.3 69.7 - - - +
322B ALA* 1.3 61.1 + - - +
324B GLY* 3.0 4.3 + - - -
325B ALA 4.2 1.1 - - - +
327B THR* 4.2 11.2 - - + -
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Residues in contact with ALA 322 (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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46B LEU* 4.5 9.4 - - + -
80B ASN 3.5 13.2 - - - +
81B CYS* 3.8 5.8 - - - -
84B ARG* 2.8 25.0 + - - -
85B HIS* 3.1 11.8 + - - -
282B LEU* 4.1 15.3 - - + -
286B ALA* 4.0 19.1 - - + -
318B TYR 3.0 20.8 + - - +
319B GLY 3.7 4.3 - - - +
320B PRO 3.3 0.2 - - - -
321B LEU* 1.3 76.8 - - - +
323B CYS* 1.3 57.6 + - - +
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Residues in contact with CYS 323 (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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45B ILE* 4.5 9.0 - - - -
84B ARG* 5.0 0.7 - - - +
85B HIS* 3.9 3.7 - - - -
92B ARG* 5.2 0.9 + - - -
286B ALA* 3.5 33.7 - - - -
289B PHE* 3.8 20.4 - - + -
290B LYS* 4.0 15.5 - - + -
295B TYR* 3.6 21.1 + - + -
319B GLY 3.2 12.9 + - - +
320B PRO 3.1 8.1 + - - +
321B LEU 3.1 0.6 - - - -
322B ALA* 1.3 78.2 - - - +
324B GLY* 1.3 61.8 + - - +
325B ALA 3.5 0.3 + - - -
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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