Contacts of the helix formed by residues 300 - 313 (chain K) in PDB entry 3Q2K
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 300 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131K GLN* 3.6 30.6 + - - +
134K ARG* 6.0 1.2 - - - +
135K ASN* 5.6 4.2 + - - -
301K HIS* 1.3 65.6 + - - -
302K PRO* 3.2 10.1 - - - +
303K LEU* 3.4 21.0 + - - +
304K TYR 3.2 14.6 + - - -
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Residues in contact with HIS 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K ILE* 3.7 21.5 - - + -
24K ASN* 3.8 29.4 + - + +
25K HIS* 3.7 22.2 + + - -
28K ALA* 3.7 4.5 - - + -
102K GLU* 2.7 28.5 + - - -
129K VAL* 3.8 13.7 - - + +
131K GLN* 3.3 31.8 + - - +
300K GLY* 1.3 68.8 - - - -
302K PRO* 1.3 68.7 - - + +
304K TYR* 3.1 7.8 + - + +
305K TYR* 3.0 39.1 + + + -
500K NAI 3.7 5.4 + - - -
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Residues in contact with PRO 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24K ASN* 4.9 2.5 - - + +
27K GLY 5.1 1.1 - - - +
28K ALA* 3.7 24.5 - - + +
31K GLN* 3.8 28.3 - - - +
32K HIS* 3.0 30.6 + - - +
300K GLY* 3.3 9.2 - - - +
301K HIS* 1.3 97.2 - - + +
303K LEU* 1.3 62.1 + - - +
304K TYR 3.4 0.2 + - - -
305K TYR* 3.6 0.7 + - - +
306K ASP 3.6 2.6 + - - -
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Residues in contact with LEU 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K HIS* 6.3 0.7 - - + -
134K ARG* 3.6 64.3 + - + +
300K GLY 3.4 18.5 + - - +
302K PRO* 1.3 78.0 - - - +
304K TYR* 1.3 65.1 + - - +
306K ASP* 3.4 30.1 - - + +
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Residues in contact with TYR 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100K VAL* 4.4 7.4 - - + -
127K PHE* 3.1 24.6 - + - +
128K VAL 2.9 22.1 + - - -
129K VAL* 3.7 26.5 - - + -
130K LYS 3.7 30.7 - - - -
131K GLN* 4.4 9.0 - - + -
134K ARG* 5.2 2.6 - - - +
300K GLY 3.2 12.0 + - - +
301K HIS* 3.1 14.8 + - - +
303K LEU* 1.3 74.4 - - - +
305K TYR* 1.3 78.7 + + - +
307K ASN* 2.9 24.2 + - + +
308K VAL* 3.2 29.7 + - + +
319K GLU* 6.0 3.6 - - + -
320K THR* 3.7 15.8 + - - -
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Residues in contact with TYR 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K PHE* 3.9 32.8 - + - -
25K HIS* 2.2 60.4 + + + +
28K ALA* 3.8 15.0 - - + +
29K ILE* 3.9 19.7 - - + -
32K HIS* 4.1 15.0 - - + -
77K VAL* 3.1 22.1 - - + +
100K VAL* 4.8 9.1 - - + +
301K HIS* 3.0 33.5 + + + +
302K PRO 3.6 1.1 + - - +
304K TYR* 1.3 79.9 - + - +
306K ASP* 1.3 55.7 + - - +
308K VAL* 2.7 13.3 + - + -
309K ILE* 2.5 44.3 + - + +
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Residues in contact with ASP 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32K HIS* 3.5 31.3 + - + +
35K ARG* 5.4 7.4 + - - +
134K ARG* 5.6 3.1 - - - -
302K PRO 3.6 1.3 + - - +
303K LEU* 3.4 28.6 - - + +
305K TYR* 1.3 75.5 - - - +
307K ASN* 1.3 59.4 + - - +
309K ILE* 3.9 3.2 - - - +
310K ASN* 2.9 46.9 + - - +
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Residues in contact with ASN 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127K PHE* 5.8 1.1 - - - -
134K ARG* 4.0 17.0 - - - +
303K LEU 3.9 0.2 + - - -
304K TYR* 2.9 17.0 + - + +
306K ASP* 1.3 81.3 - - - +
308K VAL* 1.3 66.1 + - + +
309K ILE 3.1 0.2 - - - -
310K ASN* 4.3 3.4 - - - +
311K CYS* 3.0 20.7 + - - +
316K CYS* 4.7 10.3 - - - +
317K GLU 4.0 16.2 + - - -
318K PRO* 4.0 5.0 - - - +
319K GLU* 2.7 50.0 + - - +
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Residues in contact with VAL 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13K PHE* 4.1 9.9 - - + -
100K VAL* 3.8 24.5 - - + -
127K PHE* 3.7 28.7 - - + -
304K TYR* 3.2 44.0 - - + +
305K TYR* 2.7 17.6 + - + +
307K ASN* 1.3 75.5 - - + +
309K ILE* 1.3 59.1 + - - +
311K CYS* 3.7 1.2 - - - +
312K LEU* 2.9 42.6 + - + +
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Residues in contact with ILE 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ILE* 4.6 7.2 - - + -
13K PHE* 4.3 20.6 - - + -
28K ALA 5.8 0.4 - - - +
29K ILE* 5.8 2.9 - - - +
32K HIS* 3.4 43.7 - - + +
35K ARG* 3.6 39.7 - - + +
36K ALA* 4.3 15.5 - - + -
305K TYR* 2.5 24.5 + - + +
306K ASP* 3.9 3.4 - - - +
308K VAL* 1.3 70.5 - - - +
310K ASN* 1.3 64.6 + - - +
311K CYS 2.7 6.3 + - - -
312K LEU* 3.1 4.6 + - - +
313K ARG* 3.0 29.8 + - - +
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Residues in contact with ASN 310 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35K ARG* 4.6 17.8 + - - -
306K ASP* 2.9 39.7 + - - +
307K ASN* 4.0 7.3 - - - +
309K ILE* 1.3 74.6 - - - +
311K CYS* 1.3 57.1 + - - +
313K ARG* 3.7 6.7 + - - +
315K ASP* 2.9 44.0 + - + +
316K CYS* 4.1 21.3 - - - -
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Residues in contact with CYS 311 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125K ARG* 3.7 14.3 + - - -
127K PHE* 3.6 14.8 - - + -
307K ASN* 3.0 22.7 + - - +
308K VAL 3.7 3.8 - - - +
309K ILE 2.7 3.4 + - - -
310K ASN* 1.3 75.8 - - - +
312K LEU* 1.3 63.3 + - - +
313K ARG 3.0 1.3 - - - -
314K GLY* 3.2 13.3 + - - -
316K CYS* 3.6 31.8 - - + +
318K PRO* 3.6 32.8 - - - -
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Residues in contact with LEU 312 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K ILE* 3.5 43.9 - - + +
13K PHE* 4.0 4.9 - - + -
74K ASP* 5.7 1.8 - - + -
75K ALA* 4.0 17.7 - - + -
98K HIS* 3.8 42.0 - - + +
125K ARG* 4.8 2.2 - - + -
127K PHE* 4.5 12.1 - - + -
308K VAL* 2.9 36.8 + - + +
309K ILE 3.1 1.1 + - - +
311K CYS* 1.3 76.5 - - - +
313K ARG* 1.3 58.2 + - - +
314K GLY 3.0 5.7 + - - -
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Residues in contact with ARG 313 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K ARG 4.3 17.3 + - - +
11K ILE* 3.8 21.3 - - + -
35K ARG* 4.3 36.7 - - - +
309K ILE* 3.0 20.7 + - - +
310K ASN* 3.7 5.1 - - - +
311K CYS 3.0 0.2 - - - -
312K LEU* 1.3 75.4 - - - +
314K GLY* 1.3 49.4 + - - +
315K ASP* 2.6 36.0 + - - +
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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