Contacts of the helix formed by residues 305 - 315 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B ARG* 3.9 16.4 - - - +
27B LEU* 3.8 26.7 - - + -
271B GLU* 4.2 32.1 - - + +
302B THR* 4.3 1.3 - - - +
303B GLU 3.8 7.2 - - - +
304B LEU* 1.3 90.3 - - + +
306B GLN* 1.3 62.2 + - + +
307B GLU* 3.4 18.2 - - + +
308B ALA* 3.1 11.2 + - + +
309B CYS* 2.8 26.7 + - - -
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Residues in contact with GLN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LYS* 5.3 1.4 - - - +
130B MSE 3.5 24.1 - - + +
131B TRP* 3.9 19.7 - - - +
133B HIS* 3.6 3.8 - - - +
134B ASN* 2.7 51.9 + - + +
135B PRO* 5.7 0.4 - - - +
136B ARG* 5.1 1.4 + - - -
266B ILE 3.2 25.3 + - - -
267B ILE* 4.6 2.2 - - - +
268B PRO* 3.4 23.4 - - + +
302B THR* 6.0 0.4 - - - -
304B LEU 3.6 0.8 + - - -
305B PRO* 1.3 68.6 - - - +
307B GLU* 1.3 72.7 + - - +
309B CYS* 3.1 13.0 + - - +
310B MSE 2.8 27.4 + - - +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A THR* 4.4 1.2 + - - -
20B LYS* 3.1 37.6 + - + +
21B VAL* 5.5 3.1 - - + -
23B ARG* 3.4 23.9 + - - +
24B ALA* 3.4 21.8 - - + -
130B MSE 3.4 34.4 - - + +
271B GLU* 5.0 0.7 - - - +
305B PRO* 3.8 12.6 - - + +
306B GLN* 1.3 91.2 + - - +
308B ALA* 1.3 61.5 + - + +
310B MSE 3.0 6.5 + - + +
311B VAL* 2.9 31.4 + - + +
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ALA* 3.5 23.1 - - - +
27B LEU* 3.9 15.5 - - + -
28B ALA 4.8 1.2 - - - +
304B LEU* 4.1 10.3 - - + -
305B PRO* 3.1 25.0 + - + +
307B GLU* 1.3 78.3 - - - +
309B CYS* 1.3 61.2 + - - +
311B VAL* 2.9 12.5 - - - +
312B ARG* 2.8 31.1 + - - +
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Residues in contact with CYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B HIS* 3.8 24.6 + - + +
135B PRO* 4.5 11.2 - - - -
304B LEU* 2.9 35.9 - - + -
305B PRO 2.8 31.1 + - - -
306B GLN* 3.1 11.0 + - - +
308B ALA* 1.3 77.3 - - - +
310B MSE 1.3 58.2 + - - +
312B ARG* 3.1 13.9 + - - +
313B GLU* 3.0 26.3 + - - +
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Residues in contact with MSE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B VAL* 5.1 11.7 - - + -
76B TYR* 5.3 0.7 - - + -
99B LEU* 3.5 42.0 - - + -
101B GLU* 5.6 0.9 - - - +
126B MSE 4.2 8.1 - - - -
127B ASP 4.0 4.9 - - - +
128B GLY* 3.7 31.9 - - - +
129B THR 4.2 0.4 - - - -
130B MSE 3.7 21.8 - - + -
133B HIS* 3.3 35.5 - - + +
306B GLN 2.8 10.4 + - - +
307B GLU* 3.0 13.2 + - + +
309B CYS* 1.3 72.2 - - - +
311B VAL* 1.3 65.5 + - + +
312B ARG 2.9 1.3 - - - -
313B GLU* 2.8 24.1 + - - +
314B PHE* 2.9 12.4 + - - +
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Residues in contact with VAL 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ILE* 5.5 3.8 - - + -
21B VAL* 4.2 7.4 - - + -
24B ALA* 3.0 37.2 - - + +
25B ILE* 4.1 22.2 - - + +
28B ALA* 5.3 2.5 - - - -
31B ALA* 5.4 5.6 - - + -
99B LEU* 4.1 21.3 - - + -
307B GLU* 2.9 7.7 + - + +
308B ALA* 2.9 27.8 - - - +
310B MSE 1.3 80.5 - - + +
312B ARG* 1.3 56.1 + - - +
314B PHE* 3.8 8.8 - - - +
315B ALA* 2.8 35.4 + - - +
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Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ALA* 3.2 25.1 + - - +
29B PRO* 4.9 7.4 - - - +
30B ASN* 3.0 42.3 + - - +
304B LEU* 3.4 25.8 - - + +
308B ALA 2.8 19.9 + - - +
309B CYS* 3.1 21.2 + - - +
310B MSE 2.9 0.2 - - - -
311B VAL* 1.3 80.2 - - + +
313B GLU* 1.3 58.6 + - - +
315B ALA 3.9 1.9 + - - -
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Residues in contact with GLU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B MSE 4.3 14.6 - - + -
133B HIS* 4.2 12.1 - - + +
309B CYS 3.0 11.6 + - - +
310B MSE 2.8 14.2 + - - +
312B ARG* 1.3 72.4 - - - +
314B PHE* 1.3 67.6 + - - +
315B ALA 3.8 4.0 - - - -
329B ASP* 5.1 3.3 - - - +
332B TRP* 4.4 20.4 + - + +
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Residues in contact with PHE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 6.0 0.7 - - + -
9B ILE* 5.3 12.6 - - + -
74B ALA* 3.8 18.8 - - + -
75B LEU 4.4 2.7 - - - -
97B HIS* 3.8 10.5 - - + -
98B ILE* 3.4 42.8 - - - -
99B LEU* 4.0 28.0 - - + -
124B GLN* 3.8 33.8 - - + +
126B MSE 4.0 34.2 - - + +
310B MSE 2.9 11.6 + - - +
311B VAL* 3.8 10.3 - - - +
313B GLU* 1.3 78.1 - - - +
315B ALA* 1.3 67.3 + - - +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 3.6 36.4 - - + +
9B ILE* 5.1 3.1 - - + -
30B ASN* 3.6 43.3 - - - +
31B ALA* 3.8 14.6 - - + -
311B VAL 2.8 18.9 + - - +
312B ARG 4.1 0.2 - - - -
313B GLU 3.2 6.9 - - - -
314B PHE* 1.3 85.9 - - - +
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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