Contacts of the helix formed by residues 301 - 323 (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 ILE 301 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TRP* 3.5 30.5 - - + +
46A SER* 3.8 7.9 - - - +
48A MET 5.1 3.8 - - - +
50A MET* 3.9 30.8 - - + +
52A PRO* 4.4 13.7 - - + -
81A THR* 3.6 22.4 - - + +
297A TYR* 2.8 44.7 + - + +
299A LYS 3.6 0.4 - - - -
300A THR* 1.3 87.3 - - - +
302A LEU* 1.3 60.1 + - - +
304A PRO* 3.6 3.1 - - - +
305A GLY* 2.9 27.7 + - - -
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Residues in contact with LEU 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A PRO* 3.5 38.9 - - + +
53A THR* 4.0 22.7 - - + -
81A THR 4.1 7.0 - - - +
82A GLY* 4.3 17.5 - - - +
297A TYR 3.0 7.9 + - - +
298A GLN* 3.2 39.3 - - - +
301A ILE* 1.3 75.9 - - - +
303A LYS* 1.3 64.1 + - + +
305A GLY* 3.1 1.9 + - - -
306A VAL* 2.8 39.1 + - + +
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Residues in contact with LYS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A GLN* 2.9 49.7 + - + +
299A LYS* 4.9 4.9 - - - +
302A LEU* 1.3 72.9 - - + +
304A PRO* 1.3 69.7 - - + +
306A VAL* 3.3 8.4 + - - +
307A GLU* 3.0 23.6 + - - +
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Residues in contact with PRO 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 5.6 0.6 - - - +
298A GLN 3.8 1.3 - - - +
299A LYS 3.1 27.6 - - - +
300A THR* 3.8 13.9 - - - +
301A ILE 3.6 11.2 - - - +
302A LEU 3.5 2.9 - - - -
303A LYS* 1.3 92.8 - - + +
305A GLY* 1.3 54.5 + - - +
307A GLU* 3.4 7.1 + - + +
308A ALA* 2.9 29.5 + - - +
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Residues in contact with GLY 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 5.5 1.3 - - - -
50A MET 3.0 31.5 - - - +
51A ASN* 4.0 7.0 - - - +
57A TRP* 4.6 0.9 - - - -
301A ILE 2.9 15.4 + - - -
302A LEU 3.1 0.6 + - - -
304A PRO* 1.3 75.0 - - - +
306A VAL* 1.3 64.4 + - - +
308A ALA* 3.2 7.1 + - - +
309A ASN* 3.0 23.9 + - - +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN* 3.5 27.7 + - - +
53A THR* 3.6 13.2 - - + +
302A LEU* 2.8 31.1 + - + +
303A LYS* 3.7 7.6 - - - +
305A GLY* 1.3 75.4 - - - +
307A GLU* 1.3 59.0 + - - +
309A ASN* 3.4 3.5 + - - +
310A ASN* 2.9 27.6 + - + +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303A LYS 3.0 15.5 + - - +
304A PRO* 3.8 7.6 - - + +
306A VAL* 1.3 76.0 - - - +
308A ALA* 1.3 60.5 + - - +
310A ASN* 3.2 22.4 + - - -
311A LYS* 2.9 65.1 + - + +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ARG* 3.7 37.2 - - + +
57A TRP* 3.9 7.0 - - + -
304A PRO 2.9 17.9 + - - +
305A GLY 3.2 5.6 + - - +
307A GLU* 1.3 76.4 - - - +
309A ASN* 1.3 58.3 + - - +
311A LYS* 3.3 12.3 + - - +
312A TRP* 2.9 27.9 + - - +
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Residues in contact with ASN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ASN* 2.9 34.2 - - + +
54A ASN* 2.9 29.9 + - - +
57A TRP* 3.4 42.0 + - + +
305A GLY 3.0 10.3 + - - +
306A VAL 3.5 2.2 - - - +
308A ALA* 1.3 76.0 - - - +
310A ASN* 1.3 57.7 + - - +
312A TRP* 3.3 1.6 + - - +
313A ASN* 2.9 43.9 + - - +
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Residues in contact with ASN 310 (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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306A VAL* 2.9 16.8 + - + +
307A GLU* 3.3 30.2 + - - +
308A ALA 3.2 0.2 - - - -
309A ASN* 1.3 77.4 - - - +
311A LYS* 1.3 62.3 + - - +
313A ASN* 3.2 12.4 + - - +
314A LYS* 3.1 21.8 + - - +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A GLU* 2.9 47.6 + - + +
308A ALA* 3.7 8.7 - - - +
310A ASN* 1.3 74.4 - - - +
312A TRP* 1.3 57.7 + - - +
314A LYS* 3.2 11.6 + - - +
315A LEU* 2.9 28.2 + - - +
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Residues in contact with TRP 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 3.4 25.1 - + + +
58A ILE* 3.5 30.5 - - + -
59A ASN* 3.7 19.3 - - + +
145A THR 4.8 3.8 - - - -
146A LEU* 2.8 47.4 + - + +
308A ALA 2.9 17.2 + - - +
309A ASN 3.5 4.7 - - - +
311A LYS* 1.3 75.1 - - - +
313A ASN* 1.3 79.2 + - - +
315A LEU* 3.1 11.7 + - + +
316A PHE* 2.8 62.8 + + + -
330A LEU* 5.3 3.8 - - + -
334A LEU* 4.1 13.0 - - + -
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Residues in contact with ASN 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TRP* 5.5 0.2 - - - -
309A ASN* 2.9 40.1 + - - +
310A ASN* 3.2 12.1 + - - +
312A TRP* 1.3 96.1 - - - +
314A LYS* 1.3 58.5 + - - +
316A PHE* 3.9 2.6 - - - +
317A SER* 2.9 29.1 + - - -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A ASN* 3.1 13.9 + - - +
311A LYS* 3.4 14.1 - - - +
312A TRP 3.1 0.2 - - - -
313A ASN* 1.3 77.8 - - - +
315A LEU* 1.3 62.8 + - - +
317A SER* 3.3 7.3 + - - -
318A GLU* 3.2 27.3 + - + +
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Residues in contact with LEU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A GLY 3.7 13.0 - - - +
144A PHE* 3.6 28.6 - - + -
145A THR* 3.8 35.0 - - - +
146A LEU* 4.2 10.1 - - + -
311A LYS 2.9 14.1 + - - +
312A TRP* 3.1 14.3 + - + +
314A LYS* 1.3 78.5 - - - +
316A PHE* 1.3 56.2 + - - +
318A GLU* 3.4 7.4 + - + +
319A TYR* 3.0 25.9 + - - +
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Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 4.1 13.2 - - + +
312A TRP* 2.8 48.2 + + + +
313A ASN* 3.9 4.5 - - - +
315A LEU* 1.3 72.3 - - - +
317A SER* 1.3 67.0 + - - +
319A TYR* 3.1 20.4 + + - -
320A GLN* 3.0 64.3 + - + +
327A GLY 3.8 1.8 - - - -
330A LEU* 3.7 28.5 - - + -
331A ALA* 3.8 27.4 - - + -
334A LEU* 4.0 14.1 - - + -
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Residues in contact with SER 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A ASN 2.9 18.7 + - - -
314A LYS* 3.5 9.2 - - - -
316A PHE* 1.3 77.8 - - - +
318A GLU* 1.3 63.1 + - - +
320A GLN* 3.4 20.2 + - - +
321A LYS* 3.4 30.2 + - - +
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Residues in contact with GLU 318 (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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144A PHE* 3.9 20.0 - - + -
314A LYS* 3.2 14.5 + - - +
315A LEU* 3.7 10.3 - - + +
317A SER* 1.3 77.6 + - - +
319A TYR* 1.3 59.9 + - - +
321A LYS* 3.1 25.8 + - - +
322A LYS* 2.9 36.7 + - - +
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Residues in contact with TYR 319 (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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139A TYR* 2.7 37.3 + + - +
141A LYS* 3.9 8.0 - - + +
144A PHE* 3.7 31.4 - + + -
146A LEU* 3.6 26.7 - - + -
315A LEU 3.0 14.6 + - - +
316A PHE* 3.1 20.4 + + + +
318A GLU* 1.3 76.8 - - - +
320A GLN* 1.3 53.6 + - - +
322A LYS* 3.1 2.8 + - - +
323A PHE* 2.6 56.7 + + + -
326A LEU* 3.6 26.7 - - + +
327A GLY* 3.8 29.4 - - - -
330A LEU* 5.0 2.5 - - + -
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Residues in contact with GLN 320 (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* 3.0 49.8 + - + +
317A SER* 3.7 12.1 - - - +
318A GLU 3.2 0.2 - - - -
319A TYR* 1.3 75.8 - - - +
321A LYS* 1.3 61.9 + - + +
323A PHE 4.0 7.4 - - - -
324A PRO* 3.3 24.0 - - - +
327A GLY* 3.8 23.9 + - - +
328A ALA* 5.3 1.2 - - - +
331A ALA* 3.6 23.8 - - - +
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Residues in contact with LYS 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A SER* 3.4 27.7 + - - +
318A GLU* 3.1 30.4 + - - +
320A GLN* 1.3 78.7 - - + +
322A LYS* 1.3 64.4 + - - +
324A PRO* 3.8 12.1 - - - +
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Residues in contact with LYS 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 3.6 35.7 - - + -
318A GLU* 2.9 24.9 + - - +
319A TYR 3.6 3.1 - - - +
321A LYS* 1.3 78.8 - - - +
323A PHE* 1.3 91.8 + - + +
324A PRO* 3.4 7.0 - - - +
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Residues in contact with PHE 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
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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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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