Contacts of the helix formed by residues 288 - 302 (chain A) in PDB entry 6EBT
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 288 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A ARG 3.3 0.2 + - - -
287A ILE* 1.3 77.2 - - - +
289A PHE* 1.3 64.7 + - - +
290A ALA 3.3 2.2 - - - -
291A GLU* 3.3 20.7 + - - +
292A LYS* 2.9 40.9 + - - +
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Residues in contact with PHE 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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103A ALA* 4.7 10.5 - - + -
106A VAL* 3.6 19.1 - - + -
107A THR* 4.0 20.6 - - + -
110A TYR* 3.6 21.6 + + + +
183A LYS 4.6 3.4 - - - -
184A SER* 3.4 29.4 - - - -
185A GLN* 4.8 5.4 - - + -
189A ASP* 5.5 0.7 - - - -
274A ALA* 5.0 2.7 - - + -
275A GLY* 4.2 24.9 - - - -
285A THR* 3.2 20.2 - - + +
286A ARG 3.0 20.0 + - - +
287A ILE 3.3 1.6 + - - -
288A GLY* 1.3 76.8 - - - +
290A ALA* 1.3 65.1 + - - +
292A LYS* 3.3 2.7 + - - +
293A VAL* 2.9 54.1 + - + +
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Residues in contact with ALA 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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274A ALA* 3.4 25.6 - - - +
275A GLY* 3.9 13.9 - - - +
288A GLY 3.3 0.8 - - - +
289A PHE* 1.3 81.3 - - - +
291A GLU* 1.3 71.0 + - - +
293A VAL* 4.0 2.0 - - - +
294A ALA* 3.2 23.6 + - - +
307A THR* 3.5 16.8 + - - +
311A LYS* 4.0 7.6 - - - +
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Residues in contact with GLU 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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288A GLY* 3.4 27.1 + - - +
289A PHE 3.3 0.2 - - - -
290A ALA* 1.3 84.2 + - - +
292A LYS* 1.3 59.8 + - + +
294A ALA* 3.4 2.8 + - - +
295A ALA* 3.0 29.6 + - - +
307A THR* 4.1 25.0 - - + +
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Residues in contact with LYS 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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106A VAL* 4.0 21.7 - - + +
109A ASP* 4.2 17.9 + - - +
110A TYR* 4.1 22.0 + - - +
287A ILE 5.2 3.6 + - - -
288A GLY* 2.9 27.6 + - - +
289A PHE 3.9 2.2 - - - +
291A GLU* 1.3 77.4 - - + +
293A VAL* 1.3 59.5 + - - +
295A ALA* 3.4 6.0 + - - +
296A LYS* 2.9 29.8 + - - +
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Residues in contact with VAL 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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99A LEU* 4.2 17.9 - - + -
102A ALA* 4.5 5.6 - - + -
103A ALA* 4.5 8.3 - - + +
106A VAL* 4.1 14.1 - - + -
193A THR* 5.7 0.4 - - + -
272A LEU* 5.8 0.4 - - + -
274A ALA* 3.9 25.8 - - + -
289A PHE* 2.9 56.3 + - + +
290A ALA* 4.0 3.6 - - - +
292A LYS* 1.3 75.4 - - - +
294A ALA* 1.3 58.9 + - - +
296A LYS* 3.2 4.0 + - - +
297A VAL* 2.9 35.4 + - + +
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Residues in contact with ALA 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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272A LEU* 4.2 18.6 - - + -
274A ALA* 5.8 0.4 - - + +
290A ALA 3.2 15.8 + - - +
291A GLU* 3.8 4.3 - - - +
293A VAL* 1.3 78.9 - - - +
295A ALA* 1.3 57.4 + - - +
297A VAL* 3.3 2.6 + - - +
298A ALA* 2.8 30.1 + - - +
305A PHE* 4.0 6.2 - - - +
306A VAL* 3.7 10.3 - - - +
307A THR* 3.5 31.6 - - - +
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Residues in contact with ALA 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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291A GLU 3.0 18.5 + - - +
292A LYS* 3.9 6.5 - - - +
294A ALA* 1.3 75.8 - - - +
296A LYS* 1.3 57.2 + - - +
298A ALA* 3.4 7.6 + - - +
299A ALA* 3.0 27.7 + - - +
305A PHE 5.2 1.1 - - - -
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Residues in contact with LYS 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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102A ALA* 3.5 33.9 - - + +
105A GLU* 4.0 23.3 - - + +
106A VAL* 4.6 4.3 - - + -
292A LYS 2.9 18.7 + - - +
293A VAL* 3.5 5.6 - - - +
295A ALA* 1.3 74.3 - - - +
297A VAL* 1.3 60.0 + - - +
299A ALA* 3.2 7.4 + - + +
300A LEU* 2.9 40.0 + - + +
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Residues in contact with VAL 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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98A ILE* 4.2 7.6 - - + -
99A LEU* 4.7 6.1 - - + -
102A ALA* 3.7 17.7 - - + -
197A ILE* 3.6 34.5 - - + -
272A LEU* 4.0 11.9 - - + -
293A VAL* 2.9 28.6 + - + +
294A ALA 3.7 4.0 - - - +
296A LYS* 1.3 74.8 - - - +
298A ALA* 1.3 62.7 + - - +
300A LEU* 3.3 7.0 + - - +
301A THR* 2.9 35.4 + - + +
305A PHE* 3.7 18.6 - - + -
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Residues in contact with ALA 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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294A ALA 2.8 17.2 + - - +
295A ALA* 3.6 8.3 - - - +
296A LYS 3.2 0.2 - - - -
297A VAL* 1.3 78.4 - - - +
299A ALA* 1.3 56.9 + - - +
301A THR* 3.9 1.6 - - - -
302A GLY* 2.8 30.8 + - - -
303A LEU 3.2 23.4 + - - +
304A PRO* 4.7 1.8 - - + -
305A PHE* 3.7 19.0 - - - +
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Residues in contact with ALA 299 (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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295A ALA 3.0 17.6 + - - +
296A LYS* 3.2 7.2 + - + +
298A ALA* 1.3 78.2 - - - +
300A LEU* 1.3 64.9 + - + +
301A THR 3.5 0.3 + - - -
302A GLY* 3.8 5.0 + - - -
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Residues in contact with LEU 300 (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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98A ILE* 4.0 29.4 - - + +
101A ARG* 3.7 51.6 - - + +
102A ALA* 4.1 3.8 - - + -
105A GLU* 5.2 0.7 - - - +
125A ASP* 5.7 0.4 - - - +
296A LYS* 2.9 37.4 + - + +
297A VAL 3.3 3.6 + - - +
299A ALA* 1.3 77.7 - - + +
301A THR* 1.3 60.9 + - - +
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Residues in contact with THR 301 (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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98A ILE* 3.9 35.7 - - + -
197A ILE* 4.6 1.1 - - + -
201A ILE* 4.4 9.9 - - + -
297A VAL* 2.9 20.9 + - + +
298A ALA 3.6 0.2 + - - -
300A LEU* 1.3 78.9 - - - +
302A GLY* 1.3 62.4 + - - +
303A LEU* 3.2 18.3 + - - +
305A PHE* 3.2 31.3 - - + -
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Residues in contact with GLY 302 (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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298A ALA 2.8 11.9 + - - -
299A ALA 3.8 4.1 + - - -
300A LEU 3.6 2.0 - - - -
301A THR* 1.3 77.9 - - - +
303A LEU* 1.3 65.4 + - - +
304A PRO* 4.7 0.9 - - - +
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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
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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