Contacts of the helix formed by residues 323 - 335 (chain A) in PDB entry 1GPU
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 PHE 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A LYS* 3.6 43.5 - - + -
142A PRO* 5.5 2.5 - - + -
144A PHE* 3.8 23.6 - + - -
319A TYR* 2.6 37.1 + + + +
320A GLN 3.6 3.0 - - - +
322A LYS* 1.3 106.7 - - + +
324A PRO* 1.3 57.2 - - - +
325A GLU 3.3 2.5 - - - -
326A LEU* 4.2 20.9 - - + +
327A GLY* 2.7 36.9 + - - -
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Residues in contact with PRO 324 (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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320A GLN 3.3 12.7 - - - +
321A LYS* 3.8 12.6 - - - +
322A LYS 3.4 8.1 - - - +
323A PHE* 1.3 87.2 - - - +
325A GLU* 1.3 62.9 + - + +
327A GLY* 4.0 0.2 - - - -
328A ALA* 2.9 31.9 + - - +
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Residues in contact with GLU 325 (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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323A PHE 3.3 0.6 - - - -
324A PRO* 1.3 79.2 - - + +
326A LEU* 1.3 64.3 + - + +
328A ALA* 3.2 4.9 + - - +
329A GLU* 2.9 29.3 + - - +
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Residues in contact with LEU 326 (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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138A THR* 4.4 13.2 - - + +
139A TYR* 3.9 25.5 - - + -
141A LYS* 3.6 33.9 - - - +
319A TYR* 3.6 21.5 - - + +
323A PHE* 3.5 16.3 + - + +
325A GLU* 1.3 80.5 - - + +
327A GLY* 1.3 56.9 + - - +
329A GLU* 3.4 16.3 - - - +
330A LEU* 3.0 31.2 + - - +
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Residues in contact with GLY 327 (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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316A PHE* 3.8 3.8 - - - -
319A TYR* 3.8 14.9 - - - -
320A GLN* 3.8 26.2 - - - +
323A PHE 2.7 24.1 + - - -
324A PRO 4.0 0.2 - - - -
326A LEU* 1.3 75.3 - - - +
328A ALA* 1.3 54.6 + - - +
330A LEU 3.5 0.2 + - - -
331A ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 328 (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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320A GLN* 4.7 1.7 - - - +
324A PRO 2.9 19.9 + - - +
325A GLU* 3.7 4.5 - - - +
327A GLY* 1.3 72.8 - - - +
329A GLU* 1.3 60.5 + - - +
331A ALA* 3.3 7.7 + - - +
332A ARG* 2.8 31.2 + - - +
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Residues in contact with GLU 329 (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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138A THR* 4.8 3.3 - - - +
139A TYR* 2.6 35.5 + - - +
325A GLU 2.9 18.4 + - - +
326A LEU* 3.4 17.9 - - - +
328A ALA* 1.3 77.3 - - - +
330A LEU* 1.3 61.9 + - - +
332A ARG* 3.2 15.7 + - - +
333A ARG* 3.0 26.0 + - - +
374A PRO* 3.7 33.2 - - + +
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Residues in contact with LEU 330 (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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58A ILE* 6.4 0.7 - - + -
135A LEU* 4.1 29.8 - - + -
139A TYR* 4.1 27.3 - - + -
146A LEU* 3.8 25.4 - - + -
312A TRP* 5.3 4.3 - - + -
316A PHE* 3.7 26.5 - - + -
319A TYR* 5.0 0.7 - - + -
326A LEU 3.0 16.5 + - - +
327A GLY* 4.0 2.7 - - - +
329A GLU* 1.3 72.9 - - - +
331A ALA* 1.3 61.5 + - - +
333A ARG* 3.1 11.5 + - + +
334A LEU* 2.8 54.8 + - + +
433A ALA* 4.9 1.3 - - + -
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Residues in contact with ALA 331 (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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316A PHE* 3.8 12.5 - - + -
320A GLN* 3.6 22.0 - - - +
327A GLY 2.9 18.8 + - - +
328A ALA* 3.6 7.4 - - - +
330A LEU* 1.3 76.7 - - - +
332A ARG* 1.3 63.5 + - - +
334A LEU* 3.3 4.8 + - - +
335A SER* 3.1 22.1 + - - -
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Residues in contact with ARG 332 (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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328A ALA 2.8 17.8 + - - +
329A GLU* 3.4 11.9 + - - +
331A ALA* 1.3 77.6 - - - +
333A ARG* 1.3 73.7 + - - +
335A SER* 2.5 27.6 + - - +
336A GLY 3.3 4.3 + - - -
337A GLN* 2.8 42.9 + - + +
338A LEU 4.0 1.8 - - - +
339A PRO* 3.6 38.9 - - - +
340A ALA 5.3 0.4 - - - +
374A PRO* 3.5 21.2 - - - +
375A GLU* 2.8 43.2 + - - -
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Residues in contact with ARG 333 (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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134A ASN* 5.1 2.0 + - - -
135A LEU* 4.3 3.1 - - - +
138A THR* 5.0 3.2 - - - +
139A TYR* 2.8 52.2 + - - -
329A GLU* 3.0 19.9 + - - +
330A LEU* 3.5 11.0 - - + +
332A ARG* 1.3 84.5 - - - +
334A LEU* 1.3 58.3 + - - +
336A GLY* 2.9 16.3 + - - -
374A PRO* 3.8 18.7 + - - +
375A GLU* 3.6 34.3 - - - +
433A ALA* 2.9 36.3 + - - +
434A ASN* 3.4 24.7 + - - +
435A TYR* 3.2 44.7 + - - -
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Residues in contact with LEU 334 (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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58A ILE* 3.8 38.6 - - + -
312A TRP* 4.1 20.2 - - + -
316A PHE* 4.0 26.0 - - + -
330A LEU* 2.8 37.8 + - + +
331A ALA* 3.7 5.2 - - - +
333A ARG* 1.3 72.9 - - - +
335A SER* 1.3 59.4 + - - +
336A GLY 3.1 1.6 + - - -
433A ALA* 4.2 13.2 - - + +
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Residues in contact with SER 335 (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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331A ALA 3.1 10.8 + - - -
332A ARG* 2.5 27.4 + - - -
334A LEU* 1.3 77.5 - - - +
336A GLY* 1.3 60.2 + - - +
337A GLN* 3.7 30.6 + - - +
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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