Contacts of the helix formed by residues 314 - 329 (chain A) in PDB entry 1GZD
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 ASN 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A LEU* 4.1 1.8 - - - -
80A ARG* 3.9 4.4 - - - +
305A HIS* 3.5 14.6 + - - -
306A PHE* 2.9 37.3 + - - -
309A THR* 3.0 19.2 + - - -
310A PRO 3.6 6.3 - - - +
311A LEU* 3.2 20.0 + - - +
312A GLU 3.7 0.4 - - - -
313A LYS* 1.3 75.1 - - - +
315A ALA* 1.3 67.9 + - - +
316A PRO* 3.1 25.0 - - - +
317A VAL* 3.0 15.7 + - + +
318A LEU* 2.9 24.2 + - - +
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Residues in contact with ALA 315 (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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41A LEU* 3.6 17.2 - - + +
43A LEU* 4.0 17.7 - - + -
52A LEU* 4.0 13.9 - - + +
302A MET* 5.0 0.7 - - - -
305A HIS* 2.9 19.2 + - + +
314A ASN* 1.3 71.9 - - - +
316A PRO* 1.3 69.1 - - + +
318A LEU* 3.2 3.3 + - - +
319A LEU* 3.1 23.2 + - - +
492A MET* 4.0 22.2 - - + -
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Residues in contact with PRO 316 (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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302A MET* 4.5 6.7 - - - -
305A HIS* 3.8 10.3 - - + -
306A PHE* 3.9 20.0 - - + -
314A ASN* 3.1 13.9 - - - +
315A ALA* 1.3 96.1 - - + +
317A VAL* 1.3 55.0 - - - +
319A LEU* 3.4 5.0 + - + +
320A ALA* 3.0 28.8 + - - +
492A MET* 3.7 24.5 - - + +
495A HIS* 3.7 28.9 - - + +
496A LYS* 3.7 10.4 - - - +
499A VAL* 4.8 1.1 - - - -
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Residues in contact with VAL 317 (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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71A ALA* 4.7 5.4 - - + -
76A VAL* 4.6 4.5 - - + -
80A ARG* 4.7 0.2 - - - +
306A PHE* 3.9 9.4 - - + -
311A LEU* 3.9 42.8 - - + +
314A ASN* 3.0 30.5 + - + +
316A PRO* 1.3 75.8 - - - +
318A LEU* 1.3 67.1 + - - +
320A ALA* 3.3 2.4 + - - +
321A LEU* 2.9 43.5 + - + +
499A VAL* 3.8 26.5 - - + -
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Residues in contact with LEU 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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41A LEU* 3.9 27.6 - - + -
52A LEU* 4.8 6.7 - - + -
54A TYR* 3.8 30.1 - - + +
64A MET* 3.6 28.8 - - + +
68A VAL* 5.1 2.2 - - + -
311A LEU 4.2 7.0 - - - +
312A GLU* 3.8 26.2 - - - +
313A LYS* 4.2 0.9 - - - -
314A ASN 2.9 19.0 + - - +
315A ALA* 3.7 5.2 - - - +
317A VAL* 1.3 76.6 - - - +
319A LEU* 1.3 61.8 + - - +
321A LEU* 3.3 9.7 + - + +
322A LEU* 3.0 35.1 + - + +
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Residues in contact with LEU 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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52A LEU* 3.7 33.0 - - + -
315A ALA 3.1 17.5 + - - +
316A PRO* 3.7 5.2 - - + +
317A VAL 3.3 0.2 - - - -
318A LEU* 1.3 77.1 - - - +
320A ALA* 1.3 61.1 + - - +
322A LEU* 3.5 9.2 + - + +
323A GLY* 3.2 17.2 + - - -
404A ASP* 5.0 4.3 - - - +
474A ASN* 3.7 25.7 - - + +
476A ILE* 5.1 3.6 - - + -
492A MET* 4.1 35.2 - - + -
493A TYR* 4.7 19.5 - - + +
496A LYS* 3.8 25.3 + - + -
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Residues in contact with ALA 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 PRO 3.0 17.0 + - - +
317A VAL 3.3 2.2 + - - +
319A LEU* 1.3 76.0 - - - +
321A LEU* 1.3 63.6 + - - +
323A GLY 3.2 0.7 + - - -
324A ILE* 3.1 25.1 + - + +
496A LYS* 3.6 14.7 - - - +
499A VAL* 3.4 36.3 - - + -
500A GLN* 3.2 23.4 - - + +
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Residues in contact with LEU 321 (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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64A MET* 5.1 4.3 - - + -
67A LEU* 3.2 63.2 - - + +
68A VAL* 4.0 16.6 - - + +
70A LEU* 5.1 4.9 - - + -
71A ALA* 4.3 4.3 - - + +
317A VAL* 2.9 38.7 + - + +
318A LEU* 3.7 9.2 - - + +
320A ALA* 1.3 76.6 - - + +
322A LEU* 1.3 66.3 + - - +
324A ILE* 3.3 7.6 + - + +
325A TRP* 3.1 21.0 + - - +
499A VAL* 5.6 0.2 - - + -
503A ILE* 3.9 27.1 - - + -
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Residues in contact with LEU 322 (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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54A TYR* 3.7 33.9 - - + -
57A ASN* 3.9 29.4 - - + +
59A VAL* 4.3 8.7 - - + -
64A MET* 3.9 28.7 - - + -
67A LEU* 5.0 1.8 - - + -
318A LEU* 3.0 26.6 + - + +
319A LEU* 3.9 9.2 - - + +
320A ALA 3.3 0.2 - - - -
321A LEU* 1.3 75.9 - - - +
323A GLY* 1.3 62.9 + - - +
325A TRP* 3.2 17.7 - - + +
326A TYR* 3.2 26.8 + - + -
474A ASN* 3.8 16.4 - - - +
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Residues in contact with GLY 323 (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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319A LEU 3.2 11.0 + - - -
320A ALA 3.6 3.8 - - - -
321A LEU 3.2 0.8 - - - -
322A LEU* 1.3 77.8 - - - +
324A ILE* 1.3 58.2 + - - +
326A TYR* 3.2 7.8 + - - +
327A ILE* 2.9 42.5 + - - +
335A HIS* 5.8 5.6 - - - -
402A PRO* 6.4 0.4 - - - -
496A LYS* 5.4 3.8 - - - -
500A GLN* 3.9 9.6 - - - -
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Residues in contact with ILE 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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3A LEU* 5.6 1.8 - - + -
9A PHE* 5.7 0.7 - - + -
67A LEU* 5.0 5.2 - - + -
70A LEU* 4.6 16.2 - - + -
320A ALA 3.1 14.8 + - - +
321A LEU* 3.3 8.5 + - + +
323A GLY* 1.3 72.6 - - - +
325A TRP* 1.3 68.9 + - - +
327A ILE* 4.4 1.6 - - - -
328A ASN* 2.9 47.7 + - - +
329A PHE* 3.8 13.6 - - + -
500A GLN* 3.6 25.1 - - + -
503A ILE* 3.8 42.4 - - + -
504A TRP* 3.8 16.6 - - + +
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Residues in contact with TRP 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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12A LEU* 4.0 18.2 - - + -
15A TRP* 4.2 12.8 - + - -
16A TYR* 3.8 22.2 - + + -
23A LEU* 4.0 21.5 - - + -
58A LEU 2.8 24.8 + - - -
59A VAL* 4.2 10.4 - - + +
63A VAL* 3.9 26.9 - - + -
67A LEU* 4.4 14.6 - - + +
321A LEU 3.1 13.2 + - - +
322A LEU* 3.2 15.3 - - + +
324A ILE* 1.3 79.0 - - - +
326A TYR* 1.3 76.1 + + - +
329A PHE* 3.2 61.5 - + + +
330A PHE* 3.2 27.0 + + - -
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Residues in contact with TYR 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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57A ASN* 2.8 35.3 + - - +
58A LEU* 3.0 30.0 + - + -
322A LEU* 3.2 26.0 + - + -
323A GLY* 3.2 8.7 + - - +
325A TRP* 1.3 86.7 - + - +
327A ILE* 1.3 60.0 + - + +
330A PHE* 3.3 35.0 + + + -
331A GLY 2.8 26.3 + - - -
332A CYS* 3.1 14.5 + - + -
400A MET* 4.4 7.4 - - - -
402A PRO* 3.8 34.8 - - + -
472A PRO* 3.0 23.9 - - + +
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Residues in contact with ILE 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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323A GLY* 2.9 29.2 + - - +
324A ILE 4.0 1.1 - - - +
326A TYR* 1.3 83.8 - - + +
328A ASN* 1.3 72.4 + - - +
331A GLY* 3.5 18.7 - - - -
332A CYS* 3.9 19.3 - - + +
334A THR 5.6 1.6 - - - +
335A HIS* 6.3 0.4 - - + -
373A GLN* 3.7 26.7 - - + +
374A THR 3.7 17.3 - - - +
376A PRO* 3.6 37.7 - - + -
500A GLN* 4.8 3.6 - - - +
504A TRP* 4.0 14.1 - - + -
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Residues in contact with ASN 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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3A LEU* 4.4 7.2 - - - +
9A PHE* 4.3 21.5 - - + -
324A ILE* 2.9 36.2 + - - +
327A ILE* 1.3 75.5 - - - +
329A PHE* 1.3 72.3 + - + +
331A GLY* 5.5 0.2 - - - -
372A HIS* 4.0 7.1 + - + +
373A GLN* 2.9 34.4 + - - +
504A TRP* 3.0 29.0 + - - +
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Residues in contact with PHE 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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9A PHE* 3.5 34.1 - + - -
12A LEU* 3.4 40.6 - - + -
13A GLN* 3.6 24.9 - - + -
16A TYR* 3.3 42.9 + + + -
67A LEU* 5.2 1.1 - - + -
70A LEU* 5.5 0.4 - - + -
324A ILE* 3.8 22.4 - - + -
325A TRP* 3.2 44.3 + + + +
328A ASN* 1.3 85.3 - - + +
330A PHE* 1.3 64.1 + - - +
331A GLY* 3.3 1.6 + - - -
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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