Contacts of the helix formed by residues 293 - 307 (chain B) in PDB entry 4K2S
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 293 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69B TRP* 2.8 29.9 + - - -
85B MET* 3.6 35.8 + - - +
88B ILE* 4.5 0.9 - - - -
89B ALA* 3.6 9.2 - - - -
92B ASP* 4.0 2.6 - - - +
289B LEU 3.8 0.8 + - - -
291B HIS 3.4 5.9 + - - -
292B GLY* 1.3 76.7 - - - +
294B GLY* 1.3 62.5 + - - +
297B ALA* 3.7 5.5 + - - +
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 3.3 15.5 - - - +
92B ASP* 3.7 4.7 - - - -
93B MET* 4.9 3.1 - - - -
289B LEU* 2.9 29.2 + - - -
292B GLY 3.3 0.2 - - - -
293B GLY* 1.3 78.3 - - - +
295B ILE* 1.3 61.0 + - - -
298B MET* 3.0 32.2 + - - +
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Residues in contact with ILE 295 (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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92B ASP* 2.8 6.5 + - - -
93B MET* 4.7 12.5 - - + +
96B TRP* 3.4 36.8 - - + +
107B LEU* 4.1 24.0 - - + -
111B LEU* 3.9 26.2 - - + -
289B LEU* 3.7 32.0 - - + +
294B GLY* 1.3 68.7 - - - -
296B THR* 1.3 65.8 + - - +
299B ARG* 2.9 28.8 + - + +
327B ALA* 4.3 3.4 - - + +
331B PHE* 3.8 21.0 - - + -
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Residues in contact with THR 296 (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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65B ILE* 3.6 7.8 - - - +
66B GLU* 3.9 17.0 + - - +
69B TRP* 3.7 23.1 - - + -
92B ASP* 2.6 32.5 + - - -
96B TRP* 3.1 18.9 + - - +
295B ILE* 1.3 78.6 - - - +
297B ALA* 1.3 59.6 + - - +
299B ARG* 3.8 7.9 + - - +
300B ARG* 3.3 45.5 + - - +
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B TRP* 3.6 28.9 - - + -
85B MET* 5.4 1.1 - - + -
292B GLY 3.3 20.9 - - - +
293B GLY* 3.7 5.7 + - - +
294B GLY 3.5 1.6 + - - -
296B THR* 1.3 78.9 - - - +
298B MET* 1.3 67.8 + - - +
299B ARG 3.2 0.4 - - - -
300B ARG* 3.1 13.0 + - - +
301B VAL* 3.0 26.9 + - + +
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Residues in contact with MET 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 5.4 4.7 - - + -
287B MET* 3.2 55.4 - - + +
288B PRO 4.2 9.6 - - - +
289B LEU* 3.8 23.8 - - + -
292B GLY* 3.6 16.2 - - - +
294B GLY 3.0 21.4 + - - +
297B ALA* 1.3 75.2 - - - +
299B ARG* 1.3 60.6 + - - +
301B VAL* 3.8 25.6 - - + +
302B ALA* 2.9 33.4 + - + +
312B THR* 6.4 0.9 - - + -
314B PHE* 4.1 9.2 - - + -
331B PHE* 3.5 10.3 - - + -
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Residues in contact with ARG 299 (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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96B TRP* 4.6 16.0 - - - -
110B LEU 4.8 2.6 + - - -
111B LEU* 3.7 48.4 + - + +
295B ILE* 2.9 21.8 + - + +
296B THR* 3.9 7.1 + - - +
297B ALA 3.2 0.2 - - - -
298B MET* 1.3 77.4 - - - +
300B ARG* 1.3 61.6 + - - +
302B ALA* 3.5 1.4 + - - +
303B ASP* 2.9 50.5 + - - +
331B PHE* 3.7 14.9 - - + -
334B TRP* 3.7 24.8 - - + -
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B GLU* 3.0 40.2 + - - -
69B TRP* 5.2 4.9 - - - -
70B GLN* 4.1 9.1 - - - +
270B ILE* 3.9 14.0 - - + +
296B THR* 3.3 31.6 + - - +
297B ALA* 3.1 11.2 + - - +
299B ARG* 1.3 83.5 - - + +
301B VAL* 1.3 56.1 + - - +
303B ASP* 3.4 7.2 + - - +
304B LEU* 3.0 29.5 + - - +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.8 33.9 - - + +
273B CYS* 4.3 9.4 - - - -
277B ILE* 4.4 5.0 - - + +
285B ILE* 4.1 26.7 - - + -
287B MET* 3.9 21.5 - - + -
297B ALA* 3.0 17.2 + - + +
298B MET* 3.8 26.5 - - + +
299B ARG 3.3 0.2 - - - -
300B ARG* 1.3 72.9 - - - +
302B ALA* 1.3 66.0 + - - +
304B LEU* 3.3 3.6 + - - +
305B ALA* 2.9 21.7 + - - +
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Residues in contact with ALA 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 5.4 1.6 - - - -
298B MET* 2.9 21.8 + - + +
299B ARG* 3.9 3.4 - - - +
301B VAL* 1.3 73.5 - - - +
303B ASP* 1.3 59.7 + - - +
305B ALA* 3.3 6.5 + - - -
306B SER 3.0 12.1 + - - -
312B THR* 3.9 18.6 - - + -
331B PHE* 4.0 7.9 - - + -
334B TRP* 5.5 0.2 - - + -
335B VAL* 3.8 28.3 - - + -
337B ASN* 3.0 25.3 + - - +
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Residues in contact with ASP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B ARG* 2.9 43.5 + - - +
300B ARG* 3.8 7.0 + - - +
301B VAL 3.2 0.2 - - - -
302B ALA* 1.3 76.9 - - - +
304B LEU* 1.3 63.4 + - - +
306B SER* 2.6 25.8 + - - +
307B LEU* 3.7 8.9 + - - +
334B TRP* 4.2 16.9 - - - -
335B VAL* 5.4 0.2 - - - +
336B PRO* 5.3 4.7 - - - +
337B ASN* 5.2 2.6 - - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 4.1 21.8 - - + -
274B ARG* 4.0 38.4 - - + +
277B ILE* 4.0 15.7 - - + -
278B GLN* 4.0 23.1 - - + +
300B ARG 3.0 17.5 + - - +
301B VAL 3.7 4.9 - - - +
303B ASP* 1.3 72.7 - - - +
305B ALA* 1.3 67.6 + - - +
307B LEU* 3.2 32.0 + - + +
308B TYR* 3.5 14.5 - - + -
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ILE* 3.7 19.5 - - + +
285B ILE* 4.3 7.9 - - + -
301B VAL 2.9 13.4 + - - +
302B ALA* 3.4 12.8 - - - +
304B LEU* 1.3 78.1 - - - +
306B SER* 1.3 57.4 + - - +
308B TYR* 2.9 18.9 + - - +
310B VAL* 3.0 49.2 + - + +
337B ASN* 3.8 3.1 - - - +
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Residues in contact with SER 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA 3.0 13.6 + - - -
303B ASP* 2.6 24.2 + - - +
305B ALA* 1.3 76.4 - - - +
307B LEU* 1.3 61.8 + - - +
308B TYR 3.0 1.1 + - - -
309B HIS* 3.5 12.5 + - - +
310B VAL 4.1 2.0 - - - -
336B PRO* 6.1 3.6 - - - -
337B ASN* 3.5 25.3 - - - +
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Residues in contact with LEU 307 (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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303B ASP 4.1 9.0 - - - +
304B LEU* 3.2 28.6 + - + +
305B ALA 3.2 0.2 + - - -
306B SER* 1.3 83.1 + - - +
308B TYR* 1.3 77.8 + - + +
309B HIS* 3.6 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