Contacts of the helix formed by residues 295 - 306 (chain H) in PDB entry 3GHG
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 GLY 295 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270H LYS 3.2 15.3 - - - -
271H GLN 3.6 4.6 + - - -
272H GLY* 3.2 17.9 - - - -
294H LEU* 1.3 79.6 - - - +
296H ASN* 1.3 68.8 + - - +
297H ASP 3.6 0.7 - - - -
298H LYS* 3.3 20.5 - - - +
299H ILE* 3.1 18.2 + - - +
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Residues in contact with ASN 296 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266H TRP* 5.4 0.7 - - - +
269H TYR* 3.0 29.2 + - - +
270H LYS* 3.1 6.3 + - - -
293H TRP* 3.0 35.1 - - - +
294H LEU 3.3 0.4 + - - -
295H GLY* 1.3 69.5 - - - -
297H ASP* 1.3 56.5 + - - +
299H ILE* 2.4 34.5 + - - +
300H SER 2.9 9.0 + - - -
331H VAL* 5.1 0.9 - - - +
338H TYR* 3.7 31.1 - - + -
375H PHE* 3.1 37.0 - - - -
403H TRP* 4.8 6.1 - - - -
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Residues in contact with ASP 297 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270H LYS* 3.1 52.8 + - - +
271H GLN* 4.8 2.9 - - - +
296H ASN* 1.3 75.3 - - - +
298H LYS* 1.3 72.6 + - - +
300H SER* 3.0 22.5 + - - +
301H GLN* 3.1 13.5 + - - +
304H ARG* 4.5 0.2 + - - -
333H ASN* 5.9 0.7 - - - -
334H GLU* 5.4 3.4 - - + +
338H TYR* 3.1 21.4 + - + +
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Residues in contact with LYS 298 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233H VAL* 5.8 5.4 - - + -
234H LYS* 5.3 4.3 - - - +
236H TYR* 4.0 58.3 + - + +
237H ARG 5.8 0.2 + - - -
271H GLN* 4.2 16.3 + - - +
294H LEU* 4.3 16.4 - - + +
295H GLY* 3.3 26.8 + - - +
296H ASN 2.9 0.6 + - - -
297H ASP* 1.3 86.0 + - - +
299H ILE* 1.3 56.8 + - - +
301H GLN* 3.5 10.4 + - - +
302H LEU* 2.8 29.0 + - - +
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Residues in contact with ILE 299 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252H ILE* 3.4 48.2 - - + -
293H TRP* 3.9 27.4 - - + -
294H LEU* 4.3 17.9 - - + +
295H GLY 3.1 15.9 - - - +
296H ASN* 2.4 25.3 + - - +
298H LYS* 1.3 67.6 - - - +
300H SER* 1.3 64.2 + - - +
302H LEU* 3.4 6.4 - - - +
303H THR* 2.9 36.0 + - + -
329H PHE* 4.2 11.7 - - + -
331H VAL* 4.6 7.2 - - + -
403H TRP* 5.5 3.8 - - + -
454H ILE* 4.3 2.5 - - + -
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Residues in contact with SER 300 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296H ASN 2.9 5.6 + - - -
297H ASP* 3.0 23.6 + - - +
299H ILE* 1.3 76.6 - - - +
301H GLN* 1.3 62.9 + - - +
303H THR* 2.7 18.4 + - - -
304H ARG* 2.6 44.3 + - - +
331H VAL* 3.0 31.3 - - - +
332H GLN 3.1 16.4 - - - -
333H ASN* 4.2 2.8 - - - -
338H TYR* 4.3 1.1 - - - -
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Residues in contact with GLN 301 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229H PRO* 3.4 45.3 - - - +
230H ASP* 3.8 17.1 - - - +
233H VAL* 5.1 4.3 - - + +
236H TYR* 4.6 3.6 + - - -
297H ASP 3.1 15.4 + - - +
298H LYS* 3.7 8.6 + - - +
300H SER* 1.3 80.6 + - - +
302H LEU* 1.3 69.2 + - - +
304H ARG* 3.2 20.1 + - - +
305H MET* 3.1 27.2 + - - +
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Residues in contact with LEU 302 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210H GLU* 5.5 9.6 - - + -
227H ILE* 5.1 5.8 - - + -
229H PRO* 5.7 3.1 - - + -
236H TYR* 5.0 7.4 - - - +
250H THR* 4.4 21.5 - - + +
252H ILE* 5.4 1.3 - - + -
294H LEU* 4.5 18.8 - - + -
298H LYS 2.8 16.6 + - - +
299H ILE* 3.4 7.2 - - - +
300H SER 3.1 0.2 - - - -
301H GLN* 1.3 85.6 - - - +
303H THR* 1.3 63.2 + - - +
305H MET* 3.2 35.9 + - + +
308H THR* 4.0 9.6 + - + +
454H ILE* 3.0 41.3 - - + +
456H PRO* 5.8 6.1 - - + -
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Residues in contact with THR 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H ILE* 2.9 18.5 + - + +
300H SER 2.7 19.6 + - - -
302H LEU* 1.3 76.5 - - - +
304H ARG* 1.3 55.1 + - - +
305H MET 3.3 0.2 - - - -
306H GLY 2.4 27.9 - - - +
308H THR* 3.5 12.2 + - + -
329H PHE* 3.2 54.0 - - + +
330H THR* 4.0 10.7 - - - +
331H VAL* 3.3 17.5 + - + -
454H ILE* 3.9 13.0 - - + -
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Residues in contact with ARG 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297H ASP 4.5 0.4 + - - -
300H SER* 2.6 41.1 + - - +
301H GLN* 3.1 21.8 - - - +
302H LEU 3.1 0.2 - - - -
303H THR* 1.3 78.6 + - - +
305H MET* 1.3 64.5 + - - +
306H GLY* 3.1 2.1 + - - -
330H THR* 5.3 4.3 - - - +
331H VAL 3.4 21.0 + - - +
332H GLN* 3.8 22.4 - - - +
333H ASN* 4.1 22.4 - - - +
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Residues in contact with MET 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209H LYS* 5.1 8.1 - - + +
210H GLU* 4.2 25.1 - - + -
229H PRO* 4.0 31.9 - - - +
301H GLN* 3.1 22.5 + - - +
302H LEU* 3.2 25.1 + - + +
304H ARG* 1.3 79.2 - - - +
306H GLY* 1.3 57.8 + - - +
308H THR* 5.9 0.9 - - - +
456H PRO* 4.8 12.3 - - + -
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Residues in contact with GLY 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302H LEU 4.4 0.2 + - - -
303H THR 2.4 27.6 + - - +
304H ARG* 3.1 2.3 - - - -
305H MET* 1.3 84.5 - - - +
307H PRO* 1.3 74.9 - - - +
308H THR* 3.3 5.5 + - - -
330H THR* 5.9 0.9 - - - +
456H PRO* 6.1 1.1 - - - -
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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