Contacts of the helix formed by residues 300 - 313 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131O GLN* 3.6 33.7 - - - +
134O ARG* 5.3 2.0 - - - +
135O ASN* 5.6 4.9 - - - -
301O HIS* 1.3 66.2 + - - +
302O PRO* 3.4 11.3 - - - +
303O LEU* 3.6 20.6 + - - +
304O TYR 3.2 14.6 + - - -
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Residues in contact with HIS 301 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O ILE* 3.9 19.4 - - + +
24O ASN* 3.8 24.5 + - + +
25O HIS* 3.7 30.2 + + - -
28O ALA* 3.7 16.2 - - + -
102O GLU* 3.1 20.9 + - - -
129O VAL* 3.9 12.7 - - + +
131O GLN* 3.5 32.6 + - + +
300O GLY* 1.3 71.4 - - - -
302O PRO* 1.3 75.8 - - + +
304O TYR* 2.9 16.8 + + + +
305O TYR* 2.9 19.8 + + + -
500O NAI 4.1 0.4 - - - -
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Residues in contact with PRO 302 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24O ASN 5.5 0.2 - - - +
27O GLY 5.2 0.9 - - - +
28O ALA* 3.9 23.6 - - + +
31O GLN* 3.3 30.5 - - + +
32O HIS* 3.2 27.4 + - - +
300O GLY* 3.5 11.0 - - - +
301O HIS* 1.3 93.9 - - + +
303O LEU* 1.3 64.0 + - + +
305O TYR* 3.0 8.7 + - - +
306O ASP 3.2 0.9 + - - -
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Residues in contact with LEU 303 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134O ARG* 3.7 53.1 - - + +
300O GLY 3.6 19.0 + - - +
301O HIS 3.2 0.2 - - - -
302O PRO* 1.3 80.3 - - - +
304O TYR* 1.3 64.7 + - - +
306O ASP* 3.2 27.3 + - + +
307O ASN* 3.8 3.5 + - - +
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Residues in contact with TYR 304 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100O VAL* 4.4 5.4 - - + -
127O PHE* 3.5 18.2 - + - +
128O VAL 2.8 33.6 + - - -
129O VAL* 4.0 22.2 - - + -
130O LYS 3.7 27.1 - - - -
131O GLN* 4.3 9.2 - - + -
134O ARG* 5.1 10.0 - - + +
300O GLY 3.2 10.9 + - - +
301O HIS* 2.9 14.8 + + + +
303O LEU* 1.3 79.3 - - - +
305O TYR* 1.3 72.2 + + - +
306O ASP 3.3 0.9 + - - -
307O ASN* 3.3 21.9 + - + +
308O VAL* 3.3 33.3 + - + +
319O GLU* 5.9 4.5 - - + -
320O THR* 3.8 16.8 + - - -
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Residues in contact with TYR 305 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13O PHE* 3.9 32.8 - + - -
25O HIS* 2.6 42.7 + + - +
28O ALA* 3.2 32.3 - - + +
29O ILE* 3.7 25.4 - - + +
32O HIS* 4.2 12.6 - - + -
77O VAL* 3.3 18.8 - - + +
100O VAL* 4.5 7.4 - - + +
301O HIS* 2.9 19.5 + + + +
302O PRO 3.0 8.0 + - - +
304O TYR* 1.3 81.1 - + - +
306O ASP* 1.3 55.8 + - - +
308O VAL* 3.6 13.0 - - + +
309O ILE* 2.6 44.4 + - + +
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Residues in contact with ASP 306 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32O HIS* 3.7 20.8 + - + +
35O ARG* 3.3 20.1 + - - +
302O PRO 3.2 6.1 + - - +
303O LEU* 3.3 21.0 - - + +
304O TYR 3.2 0.2 - - - -
305O TYR* 1.3 77.2 - - - +
307O ASN* 1.3 58.5 + - - +
309O ILE* 3.4 1.0 + - - +
310O ASN* 3.0 43.4 + - - +
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Residues in contact with ASN 307 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127O PHE* 4.9 3.6 - - - -
303O LEU 3.8 3.2 + - - +
304O TYR* 3.3 14.5 + - + +
305O TYR 3.3 0.2 - - - -
306O ASP* 1.3 75.8 - - - +
308O VAL* 1.3 71.7 + - - +
310O ASN* 3.8 6.6 - - - +
311O CYS* 2.9 22.9 + - - +
316O CYS* 4.0 12.1 - - - +
317O GLU 3.2 24.2 + - - -
318O PRO* 3.7 7.1 - - - +
319O GLU* 3.2 49.4 + - - +
320O THR 4.8 0.7 + - - -
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Residues in contact with VAL 308 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O PHE* 3.7 30.1 - - + -
100O VAL* 4.2 8.5 - - + -
127O PHE* 4.2 31.8 - - + -
304O TYR* 3.3 42.2 - - + +
305O TYR* 3.2 16.0 + - + +
307O ASN* 1.3 79.3 + - - +
309O ILE* 1.3 65.6 + - - +
311O CYS* 3.2 1.4 + - - +
312O LEU* 3.1 34.1 + - + +
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Residues in contact with ILE 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O ILE* 4.8 7.7 - - + +
13O PHE* 4.2 14.8 - - + -
29O ILE* 5.7 1.1 - - - -
32O HIS* 3.5 42.2 - - + +
35O ARG* 3.5 41.5 - - + +
36O ALA* 3.9 20.9 - - + -
305O TYR* 2.6 30.8 + - + +
306O ASP 3.8 2.5 - - - +
308O VAL* 1.3 77.1 - - - +
310O ASN* 1.3 63.4 + - - +
312O LEU* 3.3 5.6 + - - +
313O ARG* 2.9 35.1 + - + +
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Residues in contact with ASN 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O ARG* 2.5 32.7 + - - -
306O ASP* 3.0 37.7 + - - +
307O ASN* 3.3 2.6 + - - +
309O ILE* 1.3 76.0 - - - +
311O CYS* 1.3 58.9 + - - +
313O ARG* 3.3 8.9 + - - +
314O GLY 3.3 3.5 + - - -
315O ASP* 3.1 39.0 + - + +
316O CYS* 2.9 26.0 - - - -
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Residues in contact with CYS 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125O ARG* 2.2 48.7 + - - -
127O PHE* 3.8 24.5 - - + -
307O ASN 2.9 17.7 + - - +
308O VAL 3.6 3.1 - - - +
310O ASN* 1.3 75.2 - - - +
312O LEU* 1.3 62.6 + - - +
313O ARG 3.0 1.3 - - - -
314O GLY* 3.0 19.1 + - - -
316O CYS* 3.7 24.3 - - + +
317O GLU 4.5 1.1 - - - -
318O PRO* 4.0 12.6 - - + -
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Residues in contact with LEU 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5O PRO* 3.9 4.5 - - - +
6O ILE* 3.1 30.6 + - + +
11O ILE* 4.1 34.8 - - + -
13O PHE* 4.3 0.9 - - + -
74O ASP* 5.5 1.1 - - + -
75O ALA* 4.1 19.1 - - + -
98O HIS* 3.2 43.5 - - + +
125O ARG* 4.2 6.1 - - + +
127O PHE* 3.9 18.4 - - + -
308O VAL* 3.1 33.5 + - + +
309O ILE* 4.0 2.9 - - - +
311O CYS* 1.3 76.7 - - - +
313O ARG* 1.3 59.0 + - - +
314O GLY 3.5 0.7 + - - -
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Residues in contact with ARG 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5O PRO* 4.6 1.7 - - - +
6O ILE 4.0 20.9 + - - +
7O THR* 3.3 56.2 + - - +
9O ARG 5.6 2.2 + - - -
11O ILE* 4.9 6.1 - - + -
35O ARG* 4.3 27.8 - - - +
309O ILE* 2.9 40.3 + - + +
310O ASN* 3.4 9.4 - - - +
311O CYS 3.0 0.4 - - - -
312O LEU* 1.3 78.2 - - - +
314O GLY* 1.3 57.8 + - - +
315O ASP* 3.5 19.3 + - - +
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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