Contacts of the helix formed by residues 262 - 269 (chain E) in PDB entry 4IG9
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 ALA 262 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261E GLY* 1.3 70.5 - - - -
263E GLY* 1.3 61.1 + - - +
264E VAL 3.2 1.7 + - - -
265E SER* 3.5 11.7 + - - +
266E VAL* 3.3 21.1 + - + +
274E ARG* 6.0 4.3 - - - +
345E GLN* 5.5 2.2 - - - +
346E ASN* 3.4 13.0 + - - +
440E GLY 3.2 3.4 + - - +
441E SER* 5.0 0.2 - - - +
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Residues in contact with GLY 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262E ALA* 1.3 78.2 - - - +
264E VAL* 1.3 60.6 + - - +
265E SER 3.4 0.9 - - - -
266E VAL* 3.5 24.1 - - - +
440E GLY* 2.8 25.0 + - - -
465E ASN* 5.5 0.2 - - - -
466E ARG* 6.3 2.5 - - - -
482E CYS* 3.5 22.8 - - - +
483E ASP* 5.4 1.2 - - - +
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Residues in contact with VAL 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E THR* 4.1 15.0 - - + +
261E GLY 3.3 15.5 - - - +
263E GLY* 1.3 78.9 - - - +
265E SER* 1.3 58.2 + - - +
266E VAL* 3.7 1.3 - - - -
267E SER* 5.3 0.4 - - - -
324E SER* 2.4 32.4 + - - -
326E CYS* 3.8 24.5 - - + -
327E HIS* 3.3 27.8 - - + +
330E ILE* 5.9 0.4 - - + -
346E ASN* 3.7 10.3 - - - +
439E ILE* 3.6 44.4 - - + +
483E ASP* 5.3 1.3 - - - -
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Residues in contact with SER 265 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ALA* 3.5 9.5 + - - -
263E GLY 3.4 0.2 - - - -
264E VAL* 1.3 83.5 - - - +
266E VAL* 1.3 63.5 + - - +
267E SER 3.2 2.7 - - - -
268E CYS* 3.2 26.5 + - - +
269E GLY 4.3 1.9 + - - -
270E ILE* 4.6 12.4 + - - +
327E HIS* 3.3 21.8 + - - -
346E ASN* 4.2 4.6 + - - -
348E ASP* 3.1 26.9 + - - -
350E LEU* 3.7 3.4 - - - +
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Residues in contact with VAL 266 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262E ALA* 3.3 19.5 - - + +
263E GLY* 3.5 21.8 - - - +
264E VAL 5.1 0.2 - - - -
265E SER* 1.3 79.6 - - - +
267E SER* 1.3 65.3 + - - +
268E CYS 3.2 1.0 + - - -
269E GLY* 4.1 6.4 + - - -
270E ILE 5.5 0.2 + - - -
466E ARG* 4.8 22.7 - - - +
481E ASP* 5.1 5.8 - - - +
482E CYS* 6.0 0.7 - - + +
483E ASP* 5.8 1.8 - - - +
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Residues in contact with SER 267 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E VAL 4.9 0.7 + - - -
266E VAL* 1.3 82.9 - - - +
268E CYS* 1.3 60.4 + - - +
269E GLY* 3.3 2.6 - - - -
324E SER* 3.5 16.2 - - - -
481E ASP* 6.0 2.0 - - - -
483E ASP* 2.5 30.3 + - - -
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Residues in contact with CYS 268 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264E VAL 4.1 0.4 - - - -
265E SER* 3.2 26.8 + - - +
267E SER* 1.3 79.5 - - - +
269E GLY* 1.3 60.2 + - - +
270E ILE* 3.3 8.1 - - + -
321E PHE* 3.5 20.0 - - + +
322E GLN 3.2 30.2 + - - +
324E SER* 3.5 27.1 - - - -
350E LEU* 3.6 24.2 - - + -
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Residues in contact with GLY 269 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E SER 4.3 0.2 + - - -
266E VAL 4.1 7.1 + - - -
267E SER 3.3 4.0 - - - -
268E CYS* 1.3 78.3 - - - +
270E ILE* 1.3 63.4 + - - +
271E PRO* 3.3 10.4 - - - +
321E PHE* 3.6 10.3 - - - -
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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