Contacts of the helix formed by residues 268 - 274 (chain A) in PDB entry 6GE4
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 ARG 268 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266A ASP* 2.8 32.4 + - - +
267A ILE* 1.3 78.8 - - + +
269A GLN* 1.3 64.0 - - + +
270A ILE 3.3 0.7 + - - -
271A TYR* 3.8 34.3 + - + +
272A ASP* 4.8 2.8 - - - +
433A LYS 3.5 15.0 + - - +
434A GLU* 4.1 25.9 + - - +
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Residues in contact with GLN 269 (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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266A ASP* 3.0 31.5 + - + +
268A ARG* 1.3 79.1 - - - +
270A ILE* 1.3 59.9 + - + +
271A TYR 3.8 0.2 - - - -
272A ASP* 4.2 1.3 - - - -
89L ARG* 2.8 45.0 + - - +
90L LYS* 3.4 59.6 + - + +
91L LEU* 4.3 16.4 - - + -
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Residues in contact with ILE 270 (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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265A VAL* 5.0 4.3 - - + -
266A ASP 5.0 0.2 - - - +
267A ILE* 3.0 22.9 + - + +
269A GLN* 1.3 88.1 - - + +
271A TYR* 1.3 64.4 + - - +
272A ASP* 3.2 5.2 - - - -
273A LYS* 2.9 19.5 + - + +
274A PHE* 3.2 37.2 - - + -
281A LEU* 4.0 14.6 - - + -
295A LEU* 4.3 23.1 - - + -
412A ALA* 4.0 12.6 - - + -
414A VAL* 5.4 0.7 - - + -
431A LEU* 3.8 24.2 - - + -
86L MET* 4.4 20.0 - - + -
89L ARG* 4.5 1.3 - - - +
91L LEU* 5.1 2.5 - - + -
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Residues in contact with TYR 271 (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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267A ILE* 3.2 46.3 + - + +
268A ARG* 3.8 39.7 + - + +
269A GLN 3.8 0.2 - - - -
270A ILE* 1.3 76.6 - - - +
272A ASP* 1.3 62.6 + - - +
273A LYS 3.1 0.7 + - - -
274A PHE* 3.1 22.2 + - - +
275A PRO 5.1 0.3 - - - +
276A GLU* 4.4 10.8 - - + +
281A LEU* 4.0 13.4 - - + +
282A LYS* 3.4 66.4 + - + +
285A PHE* 3.7 15.8 - - - -
286A GLU* 5.1 1.7 + - - +
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Residues in contact with ASP 272 (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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268A ARG 4.8 1.8 + - - +
269A GLN 3.7 7.3 - - - +
270A ILE 3.8 1.4 - - - -
271A TYR* 1.3 73.2 + - - +
273A LYS* 1.3 63.8 + - - +
274A PHE 3.3 3.0 + - - +
276A GLU* 4.3 13.3 - - - +
337A PHE 4.0 5.9 - - - +
338A GLY* 3.6 12.8 + - - -
83L THR* 5.4 6.4 - - - +
89L ARG* 2.8 44.6 + - - -
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Residues in contact with LYS 273 (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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270A ILE* 2.9 18.8 + - + +
272A ASP* 1.3 90.8 - - - +
274A PHE* 1.3 66.6 + - + +
337A PHE 5.1 0.4 - - - -
338A GLY* 3.4 18.0 + - - +
390A LEU 5.3 0.2 + - - -
391A GLU* 2.8 30.1 + - - -
392A ASN* 4.5 5.3 + - - +
394A THR* 2.8 45.7 + - + +
414A VAL* 4.4 10.0 - - - +
86L MET* 3.6 41.4 - - + +
89L ARG* 3.7 17.1 - - - +
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Residues in contact with PHE 274 (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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270A ILE* 3.2 44.0 - - + -
271A TYR 3.1 13.8 + - - +
272A ASP 3.3 2.2 - - - +
273A LYS* 1.3 89.1 - - + +
275A PRO* 1.3 77.6 - - + +
276A GLU* 3.4 6.4 + - - +
281A LEU* 3.8 31.4 - - + -
335A CYS* 5.0 1.1 - - - -
338A GLY* 3.4 11.0 - - - +
394A THR* 3.4 32.1 - - + -
395A ILE 3.5 18.4 - - - -
396A LEU* 3.8 20.6 - - + -
412A ALA* 3.5 21.3 - - + -
413A TYR 4.0 6.5 - - - -
414A VAL* 4.6 7.6 - - + -
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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