Contacts of the helix formed by residues 293 - 307 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69C TRP* 2.9 31.6 + - - -
85C MET* 3.5 32.8 + - - +
88C ILE* 4.5 0.4 - - - -
89C ALA* 3.6 9.2 - - - -
92C ASP* 3.9 2.8 - - - +
289C LEU 3.8 0.8 + - - -
291C HIS 3.4 4.9 + - - -
292C GLY* 1.3 76.9 - - - +
294C GLY* 1.3 61.3 + - - +
297C ALA* 3.7 8.3 + - - +
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Residues in contact with GLY 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA* 3.2 15.3 - - - +
92C ASP* 3.7 3.8 - - - -
93C MET* 4.7 2.9 - - - -
289C LEU* 2.9 31.6 + - - -
292C GLY 3.2 0.8 - - - -
293C GLY* 1.3 78.9 - - - +
295C ILE* 1.3 66.2 + - - -
298C MET* 3.0 25.8 + - - +
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Residues in contact with ILE 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ASP* 2.8 6.0 + - - +
93C MET* 4.7 12.7 - - + +
96C TRP* 3.4 37.0 - - + +
107C LEU* 3.9 25.4 - - + -
111C LEU* 4.0 26.7 - - + -
289C LEU* 3.8 31.8 - - + +
294C GLY* 1.3 67.9 - - - -
296C THR* 1.3 65.0 + - - +
299C ARG* 3.0 28.9 + - + +
327C ALA* 4.4 4.9 - - + +
331C PHE* 4.0 18.6 - - + -
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Residues in contact with THR 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C ILE* 3.6 6.9 - - - +
66C GLU* 3.8 19.7 - - - +
69C TRP* 3.8 19.5 - - + -
92C ASP* 2.5 36.6 + - - -
96C TRP* 3.1 17.5 + - - +
295C ILE* 1.3 76.6 - - - +
297C ALA* 1.3 61.3 + - - +
299C ARG* 3.7 9.1 + - - +
300C ARG* 3.4 40.3 + - - +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69C TRP* 3.6 29.6 - - + -
85C MET* 5.3 1.6 - - + -
270C ILE* 5.7 0.2 - - - +
292C GLY 3.2 21.3 - - - +
293C GLY* 3.7 6.3 + - - +
294C GLY 3.4 1.2 + - - -
295C ILE 3.3 0.4 - - - -
296C THR* 1.3 78.8 - - - +
298C MET* 1.3 66.0 + - - +
300C ARG* 3.1 21.6 + - - +
301C VAL* 3.1 17.8 + - + +
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Residues in contact with MET 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ILE* 5.5 4.9 - - + -
287C MET* 3.3 52.7 - - + +
288C PRO 4.5 0.2 - - - -
289C LEU* 3.8 28.9 - - + -
292C GLY* 3.6 21.3 - - - +
294C GLY 3.0 22.4 + - - +
297C ALA* 1.3 73.8 - - - +
299C ARG* 1.3 61.6 + - - +
301C VAL* 3.7 24.4 - - + +
302C ALA* 2.9 33.0 + - + +
312C THR* 6.4 0.7 - - + -
314C PHE* 3.9 11.7 - - + -
331C PHE* 3.4 10.6 - - + -
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Residues in contact with ARG 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C TRP* 5.7 8.1 - - - -
110C LEU 4.8 1.8 + - - -
111C LEU* 3.1 51.4 + - + +
295C ILE* 3.0 20.9 + - + +
296C THR* 3.9 6.7 - - - +
297C ALA 3.2 0.2 - - - -
298C MET* 1.3 76.7 - - - +
300C ARG* 1.3 62.3 + - + +
302C ALA* 3.8 1.5 - - - +
303C ASP* 2.9 50.7 + - - +
331C PHE* 3.7 15.5 - - + -
334C TRP* 3.4 32.5 - - + -
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Residues in contact with ARG 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C GLU* 3.0 39.9 + - - -
69C TRP* 5.2 4.6 - - - -
70C GLN* 4.1 9.4 - - - +
270C ILE* 3.9 14.1 - - + +
296C THR* 3.4 30.2 + - - +
297C ALA* 3.1 12.5 + - - +
299C ARG* 1.3 81.0 - - + +
301C VAL* 1.3 59.9 + - - +
303C ASP* 3.5 5.9 + - - +
304C LEU* 3.0 28.9 + - - +
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ILE* 3.7 34.5 - - + +
273C CYS* 4.3 8.7 - - - -
277C ILE* 4.4 4.7 - - + +
285C ILE* 4.0 27.1 - - + -
287C MET* 3.9 21.5 - - + -
297C ALA* 3.1 15.2 + - + +
298C MET* 3.8 26.5 - - + +
300C ARG* 1.3 76.9 - - - +
302C ALA* 1.3 63.3 + - - +
304C LEU* 3.3 3.4 + - - +
305C ALA* 3.0 21.8 + - - +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285C ILE* 5.4 1.1 - - - -
298C MET* 2.9 18.8 + - + +
299C ARG 3.8 3.4 - - - +
301C VAL* 1.3 79.5 - - - +
303C ASP* 1.3 59.0 + - - +
305C ALA* 3.3 6.1 + - - +
306C SER 2.9 22.3 + - - -
312C THR* 3.9 15.9 - - + -
331C PHE* 3.9 9.9 - - + -
334C TRP* 5.5 0.4 - - + -
335C VAL* 3.9 26.5 - - + -
337C ASN* 3.0 15.2 + - - +
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Residues in contact with ASP 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C ARG* 2.9 42.0 + - - +
300C ARG* 3.9 6.0 - - - +
302C ALA* 1.3 75.9 - - - +
304C LEU* 1.3 64.3 + - - +
306C SER* 2.8 25.6 + - - +
307C LEU* 3.6 8.7 + - - +
334C TRP* 4.2 16.7 - - - -
336C PRO* 5.2 5.0 - - - +
337C ASN* 5.1 2.8 - - - +
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C ILE* 4.1 21.5 - - + -
274C ARG* 4.1 37.0 - - + +
277C ILE* 4.1 15.9 - - + -
278C GLN* 4.0 23.1 - - + +
300C ARG 3.0 18.6 + - - +
301C VAL 3.3 4.5 + - - +
303C ASP* 1.3 74.5 - - - +
305C ALA* 1.3 63.8 + - - +
307C LEU* 3.1 32.0 + - + +
308C TYR* 3.5 13.2 - - + -
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Residues in contact with ALA 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C ILE* 3.7 19.9 - - + +
285C ILE* 4.4 8.1 - - + -
301C VAL 3.0 14.1 + - - +
302C ALA* 3.3 11.9 + - - +
304C LEU* 1.3 77.7 - - - +
306C SER* 1.3 62.5 + - - +
308C TYR* 2.9 13.7 + - - -
310C VAL* 3.0 50.4 + - + +
337C ASN* 3.9 2.5 - - - +
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Residues in contact with SER 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C ALA 2.9 9.2 + - - -
303C ASP* 2.8 23.2 + - - +
304C LEU 3.2 0.2 - - - -
305C ALA* 1.3 76.5 - - - +
307C LEU* 1.3 63.3 + - - +
308C TYR 3.1 1.3 + - - -
309C HIS* 3.4 13.0 + - - +
310C VAL 4.1 2.7 - - - -
336C PRO* 6.0 3.8 - - - -
337C ASN* 3.7 30.7 - - - +
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Residues in contact with LEU 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C ASP 4.1 8.1 - - - +
304C LEU* 3.1 24.0 + - + +
305C ALA 3.1 0.2 + - - -
306C SER* 1.3 83.1 + - - +
308C TYR* 1.3 82.3 + - + +
309C HIS* 3.6 7.1 + - - -
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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