Contacts of the helix formed by residues 305 - 315 (chain A) in PDB entry 2Q4E
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 PRO 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ARG* 4.2 1.3 - - + +
27A LEU* 4.1 20.0 - - + -
271A GLU* 3.4 47.6 - - + +
302A THR 4.5 0.2 - - - -
303A GLU 4.2 4.5 - - - +
304A LEU* 1.3 91.0 - - + +
306A GLN* 1.3 54.7 + - - +
307A GLU* 3.4 22.4 - - + +
308A ALA* 3.0 18.0 + - + -
309A CYS* 2.6 32.4 + - - -
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Residues in contact with GLN 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 4.7 0.2 - - - +
130A MSE 4.0 14.2 - - + +
131A TRP* 3.8 23.4 - - - +
133A HIS* 4.1 3.3 - - - +
134A ASN* 3.3 44.2 + - + +
135A PRO* 5.8 0.2 - - - +
136A ARG* 5.2 0.7 + - - -
265A PHE 4.8 0.7 - - - +
267A ILE* 3.5 38.6 - - - +
268A PRO* 3.3 25.4 - - + +
271A GLU* 5.3 2.3 + - + +
302A THR* 5.8 0.6 + - - -
305A PRO* 1.3 68.0 - - - +
307A GLU* 1.3 71.6 + - - +
308A ALA 3.0 1.8 - - - -
309A CYS* 3.5 8.9 - - - +
310A MSE 2.6 36.3 + - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A LYS* 3.1 37.1 - - + +
21A VAL* 5.4 0.2 - - - -
23A ARG* 5.3 6.0 + - + +
24A ALA* 2.8 35.1 - - + +
130A MSE 4.1 18.2 - - + -
271A GLU* 4.1 3.2 - - - +
305A PRO* 3.6 17.0 - - + +
306A GLN* 1.3 94.9 + - - +
308A ALA* 1.3 58.9 + - + +
310A MSE 3.5 20.2 - - + +
311A VAL* 3.1 20.3 + - - +
289B THR* 3.9 18.0 - - - +
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Residues in contact with ALA 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ALA* 3.9 12.3 - - - +
27A LEU* 4.1 15.5 - - + -
28A ALA* 4.1 3.3 - - - +
304A LEU* 3.4 26.4 - - + +
305A PRO* 3.0 29.6 - - + +
306A GLN 3.0 0.2 - - - -
307A GLU* 1.3 79.6 - - - +
309A CYS* 1.3 56.6 + - - +
310A MSE 3.0 1.3 - - - -
311A VAL* 3.4 2.1 + - - +
312A ARG* 2.8 31.7 + - - +
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Residues in contact with CYS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A HIS* 3.8 20.2 - - - +
135A PRO* 4.3 21.3 - - - -
304A LEU* 2.8 51.6 - - - -
305A PRO 2.6 16.8 + - - +
306A GLN* 3.7 4.9 - - - +
308A ALA* 1.3 73.7 - - - +
310A MSE 1.3 62.3 + - - +
312A ARG* 3.6 20.9 + - - +
313A GLU* 3.4 19.8 + - - +
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Residues in contact with MSE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 4.9 6.3 - - + -
24A ALA* 4.8 1.3 - - + -
76A TYR* 6.2 0.7 - - + -
99A LEU* 4.7 12.1 - - + -
126A MSE 3.1 30.2 - - + +
127A ASP 4.7 0.2 - - - +
128A GLY* 3.9 28.3 - - - +
129A THR 4.4 2.0 - - - +
130A MSE 4.0 28.7 - - + +
133A HIS* 3.8 19.7 - - + +
306A GLN 2.6 21.6 + - - +
307A GLU* 3.5 28.9 - - + +
308A ALA 3.0 0.2 - - - -
309A CYS* 1.3 70.8 - - - +
311A VAL* 1.3 68.1 + - + +
313A GLU* 2.7 26.7 + - - +
314A PHE 3.0 8.3 + - - -
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Residues in contact with VAL 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.0 11.2 - - + -
21A VAL* 4.4 5.6 - - + -
24A ALA* 3.3 28.9 - - + -
25A ILE* 3.5 35.2 - - + +
28A ALA* 3.6 8.7 - - + -
30A ASN* 4.1 4.5 + - - +
31A ALA* 3.9 13.9 - - + +
99A LEU* 4.5 11.4 - - + -
307A GLU 3.1 6.1 + - - +
308A ALA 4.0 1.3 - - - +
310A MSE 1.3 85.6 - - + +
312A ARG* 1.3 58.0 + - - +
313A GLU 2.9 9.2 + - - -
314A PHE* 3.2 22.2 + - + +
315A ALA 4.1 2.6 + - - -
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Residues in contact with ARG 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A ALA* 3.8 6.5 - - + +
29A PRO* 4.1 18.6 - - + +
30A ASN* 3.2 35.4 + - + +
135A PRO* 6.2 0.4 - - - +
303A GLU* 5.7 4.4 + - - +
304A LEU* 3.3 32.1 - - + +
308A ALA 2.8 18.6 + - - +
309A CYS* 3.8 22.2 + - - +
310A MSE 3.1 0.2 - - - -
311A VAL* 1.3 76.8 - - - +
313A GLU* 1.3 60.8 + - - +
315A ALA* 4.7 0.9 - - - +
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Residues in contact with GLU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A MSE 5.0 3.9 - - + +
133A HIS* 4.2 22.4 - - + +
309A CYS 3.4 11.2 + - - +
310A MSE 2.7 11.3 + - - +
312A ARG* 1.3 84.7 - - - +
314A PHE* 1.3 63.1 + - - +
315A ALA* 3.0 9.4 + - - +
316A ARG* 2.7 55.1 + - - +
332A TRP* 4.7 2.8 - - + -
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Residues in contact with PHE 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 5.2 5.8 - - + -
9A ILE* 5.0 16.4 - - + -
74A ALA* 3.5 27.6 - - + -
75A LEU 3.9 9.4 - - - -
97A HIS* 4.0 7.0 - - + -
98A ILE 3.4 44.9 - - - -
99A LEU* 3.4 25.4 - - + -
124A GLN* 4.2 13.4 - - + +
126A MSE 4.2 24.5 - - + -
310A MSE 3.0 5.7 + - - +
311A VAL* 3.2 21.9 + - + +
313A GLU* 1.3 78.9 - - - +
315A ALA* 1.3 50.2 + - - +
316A ARG* 2.6 25.6 + - + +
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Residues in contact with ALA 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.4 25.4 - - + -
30A ASN* 3.0 29.8 - - + +
311A VAL 4.1 2.2 + - - -
312A ARG 4.7 2.0 - - - +
313A GLU* 3.0 7.6 - - - +
314A PHE* 1.3 73.1 - - - +
316A ARG* 1.3 64.0 + - - +
317A LEU* 3.5 14.2 + - + +
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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