Contacts of the helix formed by residues 316 - 332 (chain A) in PDB entry 3GNI
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 ASP 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A PHE* 3.8 19.2 - - - -
313A ARG* 4.5 18.0 + - + +
314A THR 3.6 2.0 - - - +
315A GLU* 1.3 76.7 + - - +
317A GLU* 1.3 60.0 + - - +
318A GLN* 3.4 13.0 + - - +
319A PHE* 3.1 33.7 + - + +
320A ASN* 3.2 27.7 + - - +
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Residues in contact with GLU 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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315A GLU* 3.4 11.0 + - - +
316A ASP* 1.3 72.3 + - - +
318A GLN* 1.3 63.1 + - - +
320A ASN* 3.7 10.6 + - + +
321A ASP* 3.2 35.9 + - - +
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Residues in contact with GLN 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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279A LYS* 4.1 9.8 + - - +
316A ASP* 3.3 10.5 + - - +
317A GLU* 1.3 74.6 - - - +
319A PHE* 1.3 56.2 + - - +
321A ASP* 3.4 4.6 + - - +
322A GLU* 2.8 64.8 + - + +
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Residues in contact with PHE 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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272A PHE* 3.5 25.1 - + + -
275A PHE* 3.8 18.6 - + - -
309A PHE* 3.5 40.8 - + - -
310A GLN* 3.5 22.9 - - + -
313A ARG* 3.7 23.3 - - + -
316A ASP* 3.1 26.2 + - - +
318A GLN* 1.3 78.2 + - - +
320A ASN* 1.3 69.9 + - - +
322A GLU* 3.8 8.6 - - - +
323A LYS* 3.0 58.7 + - + +
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Residues in contact with ASN 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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313A ARG 3.6 15.3 + - - +
314A THR* 3.7 20.4 + - - +
316A ASP 3.2 18.5 + - - +
317A GLU* 3.8 13.0 - - + +
318A GLN 3.3 0.2 - - - -
319A PHE* 1.3 80.1 - - - +
321A ASP* 1.3 68.6 + - - +
323A LYS* 3.4 16.4 + - - +
324A THR* 2.9 27.7 + - - -
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Residues in contact with ASP 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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317A GLU* 3.2 23.2 + - - +
318A GLN* 3.9 4.2 - - - +
320A ASN* 1.3 80.4 - - - +
322A GLU* 1.3 61.0 + - - +
324A THR* 3.3 10.5 + - - -
325A TYR* 3.0 29.2 + - - +
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Residues in contact with GLU 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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275A PHE* 3.3 27.5 - - + -
279A LYS* 2.9 41.1 + - + +
318A GLN* 2.8 47.6 + - + +
319A PHE* 3.8 8.6 - - - +
321A ASP* 1.3 75.2 - - - +
323A LYS* 1.3 57.2 + - - +
325A TYR* 3.2 9.6 + - + +
326A LEU* 3.0 36.3 + - + +
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Residues in contact with LYS 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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275A PHE* 3.8 25.1 - - + -
306A LEU* 3.5 28.1 + - + +
309A PHE* 2.7 34.0 + - + +
310A GLN 4.0 3.4 + - - -
311A ASN* 3.4 18.8 + - - +
313A ARG 5.6 0.2 + - - -
319A PHE* 3.0 47.6 + - + +
320A ASN* 3.7 15.2 + - - +
321A ASP 3.4 0.2 - - - -
322A GLU* 1.3 75.6 - - - +
324A THR* 1.3 61.6 + - - +
326A LEU* 3.5 4.3 + - - +
327A VAL* 3.1 29.7 + - - +
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Residues in contact with THR 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 ASN 2.9 16.7 + - - -
321A ASP* 3.4 13.4 + - - -
323A LYS* 1.3 74.5 - - - +
325A TYR* 1.3 58.4 + - - +
327A VAL* 3.4 7.4 + - - +
328A LYS* 3.1 27.9 + - + +
331A ARG* 5.2 1.3 + - - +
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Residues in contact with TYR 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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283A ALA* 3.9 37.8 + - + +
321A ASP 3.0 14.0 + - - +
322A GLU* 3.4 11.9 - - + +
324A THR* 1.3 74.7 - - - +
326A LEU* 1.3 71.5 + - + +
328A LYS* 3.3 12.2 + - + +
329A GLN* 2.9 67.7 + - + +
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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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275A PHE* 3.6 34.5 - - + -
278A PHE* 3.8 25.6 - - + -
279A LYS* 3.7 31.2 - - + +
282A VAL* 3.8 18.2 - - + -
283A ALA* 4.5 1.8 - - + +
306A LEU* 4.0 13.5 - - + -
322A GLU* 3.0 18.8 + - + +
323A LYS 3.9 3.8 - - - +
325A TYR* 1.3 86.3 - - + +
327A VAL* 1.3 65.8 + - - +
329A GLN* 3.3 4.9 + - - +
330A ILE* 3.0 34.2 + - + +
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Residues in contact with VAL 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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303A ILE* 3.8 35.3 - - + +
306A LEU* 3.6 34.3 - - + -
307A SER* 4.6 7.0 - - - +
323A LYS* 3.1 21.9 + - + +
324A THR* 3.7 5.8 - - - +
325A TYR 3.3 0.2 - - - -
326A LEU* 1.3 76.2 - - - +
328A LYS* 1.3 63.4 + - - +
330A ILE* 3.4 3.2 + - - +
331A ARG* 2.9 40.8 + - - +
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Residues in contact with LYS 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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324A THR* 3.1 15.3 + - + +
325A TYR* 3.6 14.4 - - + +
327A VAL* 1.3 76.9 - - - +
329A GLN* 1.3 65.3 + - - +
331A ARG* 3.2 30.5 + - - +
332A ASP* 2.8 58.2 + - - +
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Residues in contact with GLN 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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282A VAL* 4.0 28.4 + - + +
283A ALA 5.0 3.4 + - - -
284A ASN 6.1 0.2 - - - -
285A PRO* 6.2 1.4 - - - +
287A LYS* 4.6 8.0 - - - +
325A TYR* 2.9 64.0 + - + +
326A LEU* 3.6 5.2 - - - +
327A VAL 3.3 0.2 - - - -
328A LYS* 1.3 81.2 - - - +
330A ILE* 1.3 61.5 + - - +
332A ASP* 3.3 23.2 + - - +
333A LEU* 3.4 19.7 + - + +
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Residues in contact with ILE 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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278A PHE* 4.6 2.9 - - + -
282A VAL* 3.8 30.3 - - + -
295A LEU* 4.7 7.2 - - + +
299A GLN* 2.7 64.6 + - + +
302A LEU* 4.3 23.8 - - + -
303A ILE* 3.9 8.1 - - + -
306A LEU* 3.9 23.3 - - + -
326A LEU* 3.0 22.9 + - + +
327A VAL 4.0 2.7 - - - +
329A GLN* 1.3 72.7 - - - +
331A ARG* 1.3 56.1 + - - +
333A LEU* 3.3 22.5 + - + +
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Residues in contact with ARG 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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299A GLN* 3.6 12.6 + - - +
303A ILE* 4.1 17.6 - - + +
324A THR* 5.2 1.6 + - - +
327A VAL* 2.9 28.9 + - + +
328A LYS* 3.5 42.2 - - - +
330A ILE* 1.3 76.5 - - - +
332A ASP* 1.3 65.4 + - - +
333A LEU 3.1 6.5 + - - +
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Residues in contact with ASP 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 LYS* 2.8 54.9 + - - +
329A GLN* 3.3 14.1 + - - +
331A ARG* 1.3 84.9 + - - +
333A LEU* 1.3 63.4 + - - +
334A LYS* 3.3 12.0 + - - +
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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