Contacts of the helix formed by residues 288 - 298 (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 THR 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A SER* 3.2 41.5 + - - +
286A ASN 4.6 6.1 - - - +
287A LYS* 1.3 75.4 - - - +
289A GLN* 1.3 59.5 + - - +
290A PRO* 3.6 12.1 - - - +
291A ILE* 3.2 15.4 + - - +
292A LEU* 2.9 27.0 + - - +
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Residues in contact with GLN 289 (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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288A THR* 1.3 70.9 - - - +
290A PRO* 1.4 66.5 - - + +
292A LEU* 3.1 22.6 + - - +
293A ASP* 2.8 65.6 + - - +
296A LEU* 5.7 3.0 - - - +
336A PRO* 5.7 10.6 - - - +
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Residues in contact with PRO 290 (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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251A SER 5.5 0.4 - - - +
253A PRO* 3.8 31.6 - - + +
288A THR* 3.6 14.1 - - - +
289A GLN* 1.4 93.0 - - + +
291A ILE* 1.3 59.2 + - - +
293A ASP* 3.7 10.2 - - + +
294A ILE* 3.4 30.8 + - - +
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Residues in contact with ILE 291 (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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250A ILE 3.7 19.7 - - - +
251A SER* 3.6 10.5 - - - +
252A LYS 3.7 26.7 - - - +
253A PRO* 4.0 2.9 - - + -
256A LEU* 3.7 31.8 - - + +
281A PHE* 4.1 9.0 - - + +
287A LYS* 3.9 31.9 - - + -
288A THR* 3.2 23.5 + - - +
289A GLN 3.1 0.4 - - - -
290A PRO* 1.3 74.4 - - - +
292A LEU* 1.3 67.7 + - - +
293A ASP 3.2 0.2 - - - -
294A ILE* 3.1 12.5 + - - +
295A LEU* 3.2 18.7 + - + +
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Residues in contact with LEU 292 (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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287A LYS* 3.7 51.4 - - + +
288A THR 2.9 11.4 + - - +
289A GLN* 3.6 25.6 - - - +
291A ILE* 1.3 78.7 - - - +
293A ASP* 1.3 56.1 + - - +
295A LEU* 3.4 4.2 + - + +
296A LEU* 3.0 44.8 + - + +
333A LEU* 4.2 20.4 - - + -
334A LYS 6.1 0.4 - - - +
336A PRO* 6.5 0.9 - - + -
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Residues in contact with ASP 293 (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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289A GLN* 2.8 55.0 + - - +
290A PRO* 3.7 10.5 - - + +
292A LEU* 1.3 73.6 - - - +
294A ILE* 1.3 58.7 + - + +
296A LEU* 4.0 6.8 - - - +
297A LYS* 3.1 31.5 + - - +
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Residues in contact with ILE 294 (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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253A PRO* 3.8 35.4 - - + +
256A LEU* 3.7 22.0 - - + -
257A LYS* 5.0 2.7 - - + +
260A MET* 3.7 21.8 - - + -
290A PRO 3.4 15.2 + - - +
291A ILE 3.1 8.3 + - - +
293A ASP* 1.3 76.2 - - + +
295A LEU* 1.3 64.7 + - - +
297A LYS* 3.6 4.2 + - - -
298A ASN* 3.1 31.4 + - - +
430B GLU 5.8 0.2 - - - -
431B PHE* 4.0 33.7 - - + +
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Residues in contact with LEU 295 (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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256A LEU* 4.0 21.8 - - + -
260A MET* 4.7 2.7 - - - -
278A PHE* 4.6 3.8 - - + -
281A PHE 4.7 1.1 - - - +
282A VAL* 4.2 32.5 - - + -
287A LYS* 3.8 32.3 - - + -
291A ILE* 3.2 17.8 + - + +
292A LEU* 3.9 4.3 - - - +
294A ILE* 1.3 77.9 - - - +
296A LEU* 1.3 57.6 + - - +
298A ASN 3.4 2.9 + - - -
299A GLN* 3.0 28.6 + - - +
302A LEU* 3.8 24.8 - - + +
330A ILE* 4.7 4.9 - - + +
333A LEU* 3.6 22.5 - - + +
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Residues in contact with LEU 296 (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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289A GLN* 5.7 2.2 - - - +
292A LEU* 3.0 33.3 + - + +
293A ASP* 4.2 8.3 - - - +
295A LEU* 1.3 72.5 - - - +
297A LYS* 1.3 66.0 + - - +
298A ASN 3.4 0.3 + - - -
299A GLN* 3.4 30.0 + - - +
333A LEU* 3.7 42.4 - - + +
334A LYS 4.1 19.5 - - - +
335A ARG* 4.3 26.0 - - + +
336A PRO* 5.1 3.1 - - + -
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Residues in contact with LYS 297 (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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293A ASP 3.1 21.0 + - - +
294A ILE* 3.7 8.1 - - - +
295A LEU 3.3 0.4 - - - -
296A LEU* 1.3 76.5 - - - +
298A ASN* 1.3 62.6 + - - +
299A GLN 3.9 0.3 + - - -
301A LYS* 4.3 11.8 + - - +
430B GLU* 3.4 43.7 + - + +
431B PHE* 4.0 20.8 + - - -
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Residues in contact with ASN 298 (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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260A MET* 4.1 17.5 - - + +
294A ILE* 3.1 28.4 + - - +
295A LEU 3.5 2.5 - - - -
296A LEU 3.3 0.4 - - - -
297A LYS* 1.3 77.4 - - - +
299A GLN* 1.3 55.9 + - - +
300A ALA 3.4 2.2 - - - -
301A LYS* 3.1 18.3 + - + -
302A LEU* 2.8 49.3 + - + +
429B TRP* 3.3 15.6 - - + -
430B GLU* 2.8 46.7 + - - -
431B PHE* 4.6 1.0 - - - -
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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