Contacts of the helix formed by residues 300 - 314 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131F GLN* 3.5 33.5 - - - +
134F ARG* 6.4 0.2 - - - -
135F ASN* 5.2 6.3 - - - -
301F HIS* 1.3 64.6 + - - +
302F PRO* 3.2 12.2 - - - +
303F LEU* 3.1 13.7 + - - +
304F TYR* 2.8 24.8 + - - +
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Residues in contact with HIS 301 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F ILE* 4.0 15.6 - - + +
24F ASN* 4.1 21.0 + - + +
25F HIS* 3.5 35.0 + + - -
28F ALA* 3.7 14.1 - - + -
102F GLU* 2.9 21.9 + - - -
129F VAL* 4.0 7.7 - - + +
131F GLN* 3.4 33.1 + - + +
300F GLY* 1.3 74.5 + - - +
302F PRO* 1.3 72.9 - - + +
304F TYR* 2.9 9.4 + + + +
305F TYR* 2.9 30.8 + + + -
500F NAI 3.8 8.9 + - - -
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Residues in contact with PRO 302 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ASN* 5.5 0.4 - - + +
27F GLY 5.7 0.4 - - - -
28F ALA* 3.5 24.1 - - + +
31F GLN* 3.6 37.0 - - + +
32F HIS* 3.1 25.9 + - + -
300F GLY* 3.2 12.3 - - - +
301F HIS* 1.3 96.2 - - + +
303F LEU* 1.3 61.9 + - - +
305F TYR 3.4 4.0 + - - -
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Residues in contact with LEU 303 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134F ARG* 3.7 48.1 + - + +
300F GLY* 3.1 13.4 + - - +
302F PRO* 1.3 80.5 - - - +
304F TYR* 1.3 63.5 + - - +
306F ASP* 3.1 37.0 - - + +
307F ASN* 3.9 2.8 + - - +
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Residues in contact with TYR 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100F VAL* 4.5 6.3 - - + -
127F PHE* 3.6 11.5 - + - +
128F VAL 2.8 41.2 + - - -
129F VAL* 3.7 26.5 - - + -
130F LYS 3.8 24.2 - - - -
131F GLN* 4.1 8.7 - - + -
134F ARG* 5.7 7.4 - - + +
300F GLY 2.8 13.1 + - - +
301F HIS* 2.9 13.2 + + - +
303F LEU* 1.3 76.2 - - - +
305F TYR* 1.3 70.0 + + - +
306F ASP 3.0 4.9 + - - -
307F ASN* 3.2 20.4 + - + +
308F VAL* 3.4 30.2 + - + +
319F GLU* 4.3 18.2 - - - -
320F THR* 3.9 11.8 + - - -
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Residues in contact with TYR 305 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F PHE* 4.0 31.6 - + - -
25F HIS* 2.5 44.0 + + - +
28F ALA* 3.7 22.0 - - + +
29F ILE* 3.7 29.3 - - + +
32F HIS* 4.0 12.6 - - + -
77F VAL* 3.3 22.4 - - + +
100F VAL* 4.8 6.7 - - + -
301F HIS* 2.9 26.7 + + - +
302F PRO 3.9 4.9 - - - +
304F TYR* 1.3 81.8 - + - +
306F ASP* 1.3 64.0 + - - +
308F VAL* 3.7 14.8 - - + -
309F ILE* 3.1 31.6 + - + +
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Residues in contact with ASP 306 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32F HIS* 3.5 22.9 - - + +
35F ARG* 3.1 17.5 + - - +
302F PRO 3.5 3.0 + - - +
303F LEU* 3.1 30.6 + - + +
304F TYR 3.0 0.4 - - - -
305F TYR* 1.3 78.8 - - - +
307F ASN* 1.3 59.6 + - - +
309F ILE* 3.2 4.3 + - - +
310F ASN* 3.1 39.4 + - - +
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Residues in contact with ASN 307 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127F PHE* 5.2 2.8 - - - -
134F ARG* 4.2 18.8 - - - +
303F LEU 3.9 1.5 + - - +
304F TYR* 3.2 12.2 + - + +
306F ASP* 1.3 79.6 - - - +
308F VAL* 1.3 67.9 + - + +
310F ASN* 4.3 6.2 - - - +
311F CYS* 2.9 25.3 + - - +
316F CYS* 3.9 16.0 - - - -
317F GLU 3.5 17.3 + - - +
318F PRO* 3.8 2.9 - - - +
319F GLU* 2.9 41.4 + - + +
320F THR 4.6 0.7 + - - -
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Residues in contact with VAL 308 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F PHE* 4.2 18.8 - - + -
100F VAL* 4.0 26.0 - - + -
127F PHE* 4.1 32.1 - - + -
304F TYR* 3.4 41.7 + - + +
305F TYR* 3.8 15.9 - - + +
306F ASP 3.3 0.6 - - - -
307F ASN* 1.3 78.9 - - + +
309F ILE* 1.3 58.9 + - - +
311F CYS* 3.5 2.1 - - - +
312F LEU* 3.0 30.1 + - + +
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Residues in contact with ILE 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ILE* 4.0 17.3 - - + -
13F PHE* 4.2 22.7 - - + -
29F ILE* 6.2 0.7 - - - -
32F HIS* 3.7 28.7 - - + +
35F ARG* 3.7 29.4 - - + +
36F ALA* 3.5 24.7 - - + -
305F TYR* 3.1 23.0 + - + +
306F ASP 3.2 3.3 + - - +
307F ASN 3.1 0.4 - - - -
308F VAL* 1.3 75.5 - - - +
310F ASN* 1.3 65.7 + - - +
311F CYS 3.0 1.3 - - - -
312F LEU* 3.3 4.6 + - - +
313F ARG* 2.9 29.9 + - - +
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Residues in contact with ASN 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ARG* 3.1 19.6 + - - -
306F ASP* 3.1 37.0 + - - +
307F ASN* 4.0 4.2 - - - +
309F ILE* 1.3 74.3 - - - +
311F CYS* 1.3 66.5 + - - +
313F ARG* 2.7 22.8 + - - +
314F GLY 3.1 12.6 + - - -
315F ASP* 3.4 18.9 + - - +
316F CYS* 3.1 29.7 - - - -
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Residues in contact with CYS 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F ARG* 3.6 23.3 + - - -
127F PHE* 3.8 14.1 - - + -
307F ASN 2.9 20.0 + - - +
308F VAL 3.5 5.2 - - - +
309F ILE 3.0 0.2 - - - -
310F ASN* 1.3 81.4 - - - +
312F LEU* 1.3 63.1 + - - +
313F ARG 3.2 0.2 + - - -
314F GLY* 3.8 10.4 + - - -
316F CYS* 3.6 22.9 - - + +
317F GLU 4.6 1.3 - - - +
318F PRO* 3.3 43.1 - - + -
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Residues in contact with LEU 312 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F ILE* 3.9 38.0 - - + +
13F PHE* 4.7 0.7 - - + -
74F ASP* 5.2 2.5 - - + -
75F ALA* 4.0 21.8 - - + -
98F HIS* 3.6 40.8 - - + +
125F ARG* 4.4 6.5 - - + +
127F PHE* 4.2 17.9 - - + -
308F VAL* 3.0 27.0 + - + +
309F ILE* 4.1 3.8 - - - +
310F ASN 3.3 0.2 - - - -
311F CYS* 1.3 76.2 - - - +
313F ARG* 1.3 66.1 + - - +
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Residues in contact with ARG 313 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ARG 5.9 1.7 + - - +
11F ILE* 5.0 9.2 - - + -
35F ARG* 3.5 49.7 + - - +
309F ILE* 2.9 29.9 + - + +
310F ASN* 2.7 18.5 + - - +
312F LEU* 1.3 82.7 - - - +
314F GLY* 1.3 56.7 + - - +
315F ASP* 4.3 15.9 + - - +
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Residues in contact with GLY 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310F ASN 3.1 1.2 + - - -
311F CYS 4.2 6.1 - - - -
312F LEU 3.7 0.2 - - - -
313F ARG* 1.3 81.5 - - - +
315F ASP* 1.3 70.3 + - - +
316F CYS 3.3 6.6 + - - +
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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