Contacts of the helix formed by residues 304 - 321 (chain C) in PDB entry 3P9K
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 ASN 304 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302C GLU* 3.3 30.6 + - - +
303C ALA* 1.3 74.0 - - - +
305C PRO* 1.3 72.4 - - + +
306C SER* 2.9 14.3 + - - -
307C SER* 2.8 33.6 + - - -
308C GLN* 2.9 39.3 + - - +
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Residues in contact with PRO 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C ASN* 1.3 89.7 - - + +
306C SER* 1.3 56.9 + - - +
308C GLN* 3.6 9.8 - - - +
309C GLY* 3.0 23.2 + - - -
352C ASN* 4.6 1.6 + - - -
15D ASP 5.6 1.1 - - - +
18D MET* 4.7 20.8 - - + +
19D PHE* 4.9 12.6 - - + +
22D GLN* 3.5 28.9 - - - +
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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
----------------------------------------------------------
304C ASN* 2.9 14.0 + - - -
305C PRO* 1.3 77.9 - - - +
307C SER* 1.3 63.1 + - - -
310C VAL* 3.2 14.3 + - - +
352C ASN* 2.7 45.6 + - - +
18D MET* 4.2 24.2 - - - +
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Residues in contact with SER 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C PRO* 4.1 15.0 - - - -
301C PRO* 4.0 18.8 - - - -
302C GLU 2.7 28.3 + - - -
303C ALA* 4.0 1.7 - - - -
304C ASN* 2.8 20.2 + - - -
306C SER* 1.3 70.0 - - - +
308C GLN* 1.3 70.6 + - - +
310C VAL* 3.2 6.0 + - - +
311C PHE* 3.1 38.2 + - - -
83D SER* 5.1 0.7 - - - -
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Residues in contact with GLN 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303C ALA* 4.5 2.8 - - - +
304C ASN* 2.9 38.3 + - - +
305C PRO* 3.6 2.4 - - - +
307C SER* 1.3 75.1 + - - +
309C GLY* 1.3 58.1 + - - +
311C PHE* 3.1 5.6 + - - +
312C HIS* 2.9 34.6 + - - -
22D GLN* 2.7 34.0 + - - +
83D SER* 2.7 47.7 + - - +
84D TYR* 3.4 32.2 - - + +
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Residues in contact with GLY 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305C PRO 3.0 20.8 + - - -
306C SER 3.9 1.6 - - - -
307C SER 3.1 0.2 - - - -
308C GLN* 1.3 78.2 - - - +
310C VAL* 1.3 60.7 + - - +
312C HIS* 3.2 25.7 - - - +
313C VAL* 3.4 13.7 + - - +
352C ASN* 4.5 7.0 - - - -
18D MET 6.0 0.2 - - - -
21D LEU* 6.0 2.0 - - - -
22D GLN* 5.0 10.9 - - - +
25D SER* 5.3 0.4 + - - -
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Residues in contact with VAL 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C CYS* 4.0 25.4 - - + -
296C ILE 4.2 16.6 - - - +
297C LEU* 3.6 26.7 - - + +
298C PRO* 4.6 6.3 - - + -
306C SER 3.2 16.4 - - - +
307C SER* 3.2 9.0 + - - +
309C GLY* 1.3 73.9 - - - +
311C PHE* 1.3 63.8 + - - +
313C VAL* 3.5 5.6 + - - +
314C ASP* 3.1 16.3 + - - +
326C GLU* 3.6 12.5 - - + +
352C ASN* 3.6 24.9 - - + +
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Residues in contact with PHE 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU* 3.8 25.4 - - + -
298C PRO* 4.3 12.6 - - + -
301C PRO* 4.1 23.6 - - + -
307C SER* 3.1 25.0 + - - -
308C GLN 3.1 4.9 + - - +
310C VAL* 1.3 75.1 - - - +
312C HIS* 1.3 66.8 + - - +
314C ASP* 3.2 7.0 + - + +
315C MET* 3.0 26.5 + - - +
328C TYR* 5.3 1.1 - - - -
76D ARG 5.9 0.2 - - - +
79D ARG* 3.6 45.8 - - + -
80D LEU* 3.7 20.4 - - + +
83D SER* 3.5 31.9 - - - -
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Residues in contact with HIS 312 (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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308C GLN 2.9 26.9 + - - -
309C GLY* 3.2 11.2 - - - +
311C PHE* 1.3 75.6 - - - +
313C VAL* 1.3 63.6 + - + +
315C MET* 3.0 7.1 + - - +
316C ILE* 2.9 26.0 + - - +
22D GLN* 3.3 33.0 + - + +
25D SER* 2.9 41.5 + - - +
26D SER* 4.2 5.8 - - - -
28D VAL* 3.8 18.2 - - + +
29D LEU* 5.2 2.2 + - + +
80D LEU* 3.8 15.9 - - + -
84D TYR* 2.7 33.2 + - - -
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Residues in contact with VAL 313 (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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263C TRP* 5.1 7.9 - - + +
266C HIS* 3.9 18.6 - - + +
295C CYS* 4.9 11.4 - - - -
309C GLY 3.4 14.8 + - - +
310C VAL* 3.8 7.9 - - - +
311C PHE 3.3 0.4 - - - -
312C HIS* 1.3 77.5 - - + +
314C ASP* 1.3 57.2 + - - +
316C ILE* 3.0 9.6 + - - +
317C MET* 2.8 35.4 + - + +
326C GLU* 2.8 28.5 - - - +
603C CIY 4.3 27.4 - - + +
25D SER* 5.5 1.1 - - - +
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Residues in contact with ASP 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C LEU* 4.9 0.9 - - + -
310C VAL 3.1 10.2 + - - +
311C PHE* 3.5 13.5 - - + +
312C HIS 3.2 0.4 - - - -
313C VAL* 1.3 77.1 - - - +
315C MET* 1.3 58.4 + - - +
317C MET* 3.2 2.6 + - - +
318C LEU* 3.0 11.1 + - - +
325C ARG* 3.6 2.1 + - - +
326C GLU* 3.0 45.7 + - + +
76D ARG* 3.0 61.8 + - - +
79D ARG* 3.0 30.3 + - - +
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Residues in contact with MET 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C TRP* 3.7 12.2 - - + -
140C LEU* 3.8 22.0 - - + -
311C PHE 3.0 14.7 + - - +
312C HIS 3.5 7.6 - - - +
314C ASP* 1.3 77.4 - - - +
316C ILE* 1.3 58.9 + - - +
318C LEU* 3.2 32.6 + - + +
319C ALA* 2.9 29.6 + - - +
28D VAL* 3.7 13.2 - - + -
32D THR* 3.6 16.8 - - + +
76D ARG* 3.7 24.2 - - - +
77D ILE* 3.9 14.6 - - + -
80D LEU* 3.9 24.5 - - + -
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Residues in contact with ILE 316 (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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128C ASN* 3.6 23.6 - - + +
137C TRP* 4.7 6.3 - - + -
312C HIS 2.9 17.3 + - - +
313C VAL* 3.0 13.2 + - - +
315C MET* 1.3 79.1 - - - +
317C MET* 1.3 74.0 + - + +
319C ALA* 3.4 3.4 + - - -
320C HIS* 3.2 45.0 + - + +
603C CIY 3.8 26.2 - - + +
25D SER* 3.8 26.9 - - - -
28D VAL* 3.8 13.0 - - + -
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Residues in contact with MET 317 (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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266C HIS* 3.4 28.3 - - + +
267C ASP* 3.3 12.3 - - - +
313C VAL* 2.8 20.1 + - + +
314C ASP* 3.5 6.3 - - - +
316C ILE* 1.3 84.8 - - + +
318C LEU* 1.3 65.6 + - - +
321C ASN* 3.0 59.9 + - - +
324C GLY* 3.5 23.3 - - - +
325C ARG* 3.7 4.3 - - - +
326C GLU* 3.7 13.7 - - - +
603C CIY 3.6 34.8 - - + -
76D ARG* 4.0 0.9 - - - +
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Residues in contact with LEU 318 (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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140C LEU* 4.1 18.6 - - + -
149C ILE* 4.4 4.0 - - - +
150C PRO* 3.4 15.0 - - - +
314C ASP 3.0 8.4 + - - +
315C MET* 3.2 38.8 + - + +
317C MET* 1.3 79.3 - - - +
319C ALA* 1.3 62.8 + - - +
320C HIS 3.5 0.2 + - - -
321C ASN 4.6 1.6 - - - +
324C GLY 4.4 0.9 - - - -
73D MET* 3.6 43.7 - - + +
76D ARG* 3.4 35.8 - - + +
77D ILE* 4.3 9.9 - - + -
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Residues in contact with ALA 319 (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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136C SER* 3.7 7.7 - - - -
137C TRP* 4.0 26.7 - - + -
140C LEU* 5.5 2.7 - - + -
150C PRO* 3.2 16.6 - - + +
151C PHE* 3.0 25.6 + - - +
315C MET 2.9 16.0 + - - +
316C ILE 3.8 4.3 - - - +
317C MET 3.3 0.2 - - - -
318C LEU* 1.3 79.7 - - - +
320C HIS* 1.3 75.3 + - + +
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Residues in contact with HIS 320 (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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128C ASN* 5.4 0.8 + - - -
133C LEU* 3.2 51.5 - - + +
136C SER* 2.8 34.0 + - - -
137C TRP* 4.9 7.8 + - - -
149C ILE* 3.6 8.9 - - - +
151C PHE* 3.6 26.4 - - + +
152C ASN* 4.2 3.6 + - - -
159C ALA* 3.7 16.2 + - + +
316C ILE* 3.2 41.8 + - + +
319C ALA* 1.3 85.8 - - + +
321C ASN* 1.3 70.9 + - - +
322C PRO* 4.3 0.7 - - - +
603C CIY 5.4 5.6 - + + -
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Residues in contact with ASN 321 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C ILE* 3.8 14.5 - - - +
159C ALA* 4.2 10.6 - - - +
160C PHE* 4.4 8.0 - - - -
267C ASP* 3.1 34.6 + - - +
317C MET* 3.0 56.3 + - - +
318C LEU* 4.6 2.4 - - - +
320C HIS* 1.3 89.3 - - - +
322C PRO* 1.3 62.0 - - + +
323C GLY* 2.8 16.5 + - - -
324C GLY* 3.6 3.3 + - - +
603C CIY 3.5 11.8 + - - -
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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
------------------------------------------------------------
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