Contacts of the helix formed by residues 324 - 334 (chain B) in PDB entry 3KG2
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 324 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B HIS* 6.0 0.4 - - - -
322B PRO 3.4 5.9 + - - -
323B TRP* 1.3 70.3 - - - +
325B GLN* 1.3 60.8 + - - +
326B GLY 3.0 2.3 + - - -
327B VAL* 3.2 28.2 + - - +
328B GLU* 4.1 5.5 + - - +
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Residues in contact with GLN 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305B GLU 5.1 1.8 - - - +
306B ILE* 3.7 30.7 - - + +
323B TRP* 2.9 29.4 + - + +
324B GLY* 1.3 77.0 - - - +
326B GLY* 1.3 58.3 + - - +
327B VAL 3.3 0.2 - - - -
328B GLU* 3.6 9.5 + - - +
329B ILE* 3.2 26.2 + - - +
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Residues in contact with GLY 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B HIS* 3.7 15.8 - - - +
95B SER* 4.4 1.0 + - - -
109B PHE* 3.6 14.8 - - - -
323B TRP* 2.9 21.9 + - - -
325B GLN* 1.3 76.6 - - - +
327B VAL* 1.3 64.8 + - - +
328B GLU 3.1 0.9 - - - -
329B ILE* 3.2 14.7 + - - +
330B GLU* 3.2 17.2 + - - +
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B HIS* 3.6 27.1 - - + +
109B PHE* 4.3 9.2 - - + -
324B GLY* 3.2 19.7 + - - +
326B GLY* 1.3 77.0 - - - +
328B GLU* 1.3 65.9 + - + +
330B GLU* 3.6 9.2 + - - +
331B ARG* 3.3 20.8 + - + +
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Residues in contact with GLU 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B LEU* 4.3 6.7 - - + +
304B ILE* 3.8 42.8 - - + +
306B ILE* 4.4 6.7 - - + -
324B GLY 4.8 6.5 - - - +
325B GLN* 3.6 12.0 + - - +
326B GLY 3.1 0.4 - - - -
327B VAL* 1.3 80.8 - - + +
329B ILE* 1.3 63.6 + - - +
330B GLU 3.1 1.6 - - - -
331B ARG* 3.3 11.8 + - - +
332B ALA* 3.1 22.7 + - - +
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Residues in contact with ILE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B TYR* 3.3 39.5 - - + +
72B ALA* 4.7 4.7 - - + -
95B SER* 3.9 12.3 - - - +
295B ALA* 6.4 0.2 - - + -
299B LEU* 4.2 10.8 - - + -
306B ILE* 4.0 23.6 - - + -
323B TRP* 3.7 25.1 - - + -
325B GLN 3.2 18.2 - - - +
326B GLY* 3.2 8.2 + - - +
328B GLU* 1.3 76.9 - - - +
330B GLU* 1.3 61.2 + - - +
332B ALA* 3.4 2.7 + - + +
333B LEU* 3.2 33.2 + - + +
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Residues in contact with GLU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B SER* 3.9 8.0 + - - +
108B PRO* 4.2 7.8 - - - +
109B PHE* 3.4 61.4 + - + -
111B ILE* 5.2 6.6 - - + +
326B GLY 3.2 11.3 + - - +
327B VAL* 3.7 12.6 - - - +
328B GLU 3.1 0.6 - - - -
329B ILE* 1.3 73.5 - - - +
331B ARG* 1.3 59.9 + - - +
332B ALA 2.9 9.3 + - - -
333B LEU* 3.3 4.9 + - - +
334B LYS* 3.0 29.2 + - + +
349B GLN 4.3 13.3 - - - +
350B ASN 5.1 1.7 - - - +
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Residues in contact with ARG 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B VAL* 3.3 11.0 + - + +
328B GLU* 3.3 17.6 + - - +
330B GLU* 1.3 78.7 - - - +
332B ALA* 1.3 56.8 + - - +
334B LYS* 4.8 4.3 - - - -
335B GLN* 3.1 26.6 + - - +
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ALA* 3.7 19.0 - - + +
298B ASN* 5.1 5.4 + - + -
299B LEU* 3.3 39.3 - - + -
328B GLU 3.1 5.5 + - - +
329B ILE* 3.5 10.1 - - + +
330B GLU 2.9 0.6 - - - -
331B ARG* 1.3 77.3 - - - +
333B LEU* 1.3 65.8 - - - +
335B GLN* 3.1 14.2 + - - +
336B VAL* 3.1 15.2 + - - +
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ALA* 4.9 2.7 - - + -
95B SER* 3.7 27.8 - - - +
97B ILE* 3.7 19.5 - - + -
111B ILE* 4.1 19.1 - - + -
291B VAL* 3.9 13.1 - - + +
292B MET* 3.8 28.3 - - + -
295B ALA* 3.4 25.1 - - + -
329B ILE* 3.2 24.5 + - + +
330B GLU* 4.0 3.4 - - - +
332B ALA* 1.3 77.5 - - - +
334B LYS* 1.3 62.5 + - - +
336B VAL* 3.2 19.6 + - - +
347B PHE* 3.8 11.8 - - - -
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Residues in contact with LYS 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ILE* 4.5 12.5 - - + +
330B GLU* 3.0 22.3 + - + +
331B ARG* 4.8 4.0 - - - -
333B LEU* 1.3 77.3 - - - +
335B GLN* 1.3 59.6 + - - +
336B VAL 3.3 1.1 - - - +
347B PHE* 3.6 33.4 + - + +
348B ASP 3.9 19.1 - - - +
349B GLN* 5.3 6.3 - - - +
350B ASN 6.1 0.7 - - - -
351B GLY* 5.7 0.4 - - - -
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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