Contacts of the helix formed by residues 298 - 316 (chain B) in PDB entry 3MIZ
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 298 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B PRO* 4.0 13.9 - - + -
296B ALA* 3.3 10.5 - - + +
297B LEU* 1.3 77.8 - - - +
299B TYR* 1.3 52.3 + - - +
300B TYR 3.4 2.5 - - - -
301B ASP* 3.3 19.3 + - + +
302B LEU* 2.7 40.9 + - + +
326B VAL* 3.8 29.4 - - + +
327B SER 3.6 23.6 - - - +
328B CYS* 3.8 11.2 - - - -
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Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B TYR* 3.1 32.6 - - - +
75B SER* 3.4 19.9 + - - -
77B ASP* 3.7 20.0 - - + -
78B ILE* 2.9 41.9 - - + +
125B MSE 3.8 12.1 + - - -
126B TYR* 4.9 2.6 - - - +
127B ARG 5.5 0.5 + - - -
145B ASN* 3.8 25.6 + - - -
159B PRO* 5.0 2.2 - - + +
279B ASP* 5.8 2.9 - - + -
297B LEU* 2.8 53.0 + - + +
298B PRO* 1.3 72.4 - - - +
300B TYR* 1.3 63.6 + - - +
302B LEU* 3.2 7.7 + - + -
303B GLY 3.1 10.4 + - - -
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Residues in contact with TYR 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ASP* 3.5 15.1 + - - +
80B ARG* 3.1 48.2 - - - +
81B GLY* 3.4 33.2 - - - -
84B ASP* 2.9 29.6 + - + +
298B PRO 3.4 0.4 - - - -
299B TYR* 1.3 78.1 - - - +
301B ASP* 1.3 78.7 + - - +
303B GLY 3.2 2.9 + - - -
304B ARG* 3.1 37.1 + - + +
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Residues in contact with ASP 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B PRO* 3.3 21.2 + - + +
300B TYR* 1.3 90.7 - - - +
302B LEU* 1.3 60.8 + - - +
304B ARG* 3.3 29.9 + - - +
305B GLU* 2.8 38.0 + - + +
326B VAL* 5.4 6.5 - - + -
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Residues in contact with LEU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 3.6 9.4 - - + -
144B ILE* 3.9 16.5 - - + +
145B ASN* 4.4 2.7 - - + +
157B ILE* 3.6 37.2 - - + +
158B GLU 3.9 12.3 - - - -
159B PRO* 3.7 30.1 - - + -
298B PRO* 2.7 31.5 + - + +
299B TYR* 3.2 28.2 + - + +
301B ASP* 1.3 73.1 - - - +
303B GLY* 1.3 58.6 + - - +
305B GLU* 4.0 3.3 - - - +
306B GLY* 2.9 26.3 + - - -
326B VAL* 3.8 15.5 - - + +
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Residues in contact with GLY 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B ILE* 3.6 28.7 - - - +
82B ILE* 3.5 18.9 - - - +
144B ILE* 4.4 2.4 - - - +
299B TYR 3.1 10.3 + - - -
300B TYR 3.2 1.8 + - - -
302B LEU* 1.3 77.1 - - - +
304B ARG* 1.3 58.3 + - - +
306B GLY* 3.9 0.2 - - - -
307B ALA* 3.0 31.7 + - - +
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Residues in contact with ARG 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 4.4 15.1 + - - -
81B GLY* 3.7 17.1 - - - +
85B TRP* 4.0 26.2 - - + +
300B TYR* 3.1 32.3 + - + +
301B ASP* 3.3 37.1 + - - +
303B GLY* 1.3 74.9 - - - +
305B GLU* 1.3 92.5 + - - +
307B ALA* 3.8 0.3 + - - +
308B LYS* 3.2 26.9 + - + +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 3.3 37.1 - - - +
157B ILE* 3.9 21.1 - - + -
301B ASP* 2.8 21.1 + - + +
302B LEU 4.0 0.2 - - - +
304B ARG* 1.3 94.0 + - - +
306B GLY* 1.3 60.2 + - - +
308B LYS* 3.3 10.7 + - - +
309B TRP* 2.8 31.7 + - - +
324B ARG* 2.8 36.8 + - - -
326B VAL* 5.6 4.0 - - + -
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Residues in contact with GLY 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LEU* 3.9 6.9 - - - +
142B VAL* 4.1 10.2 - - - +
144B ILE* 4.0 12.1 - - - -
157B ILE* 4.5 7.7 - - - +
302B LEU 2.9 18.8 + - - -
303B GLY 3.9 0.4 - - - -
305B GLU* 1.3 77.5 - - - +
307B ALA* 1.3 51.2 + - - +
309B TRP* 3.2 6.9 + - - +
310B LEU* 2.7 36.0 + - - +
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Residues in contact with ALA 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 4.1 5.1 - - + -
82B ILE* 4.3 19.3 - - + -
85B TRP* 3.6 34.0 - - + -
121B LEU* 4.2 14.7 - - + +
303B GLY 3.0 19.0 + - - +
304B ARG 4.0 2.0 - - - +
306B GLY* 1.3 74.1 - - - +
308B LYS* 1.3 58.2 + - - +
310B LEU* 3.2 4.9 + - - +
311B ASN* 2.9 28.2 + - - +
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 5.7 6.8 + - - +
320A TYR* 3.8 31.0 - - + +
85B TRP* 3.6 31.3 - - + +
304B ARG* 3.2 20.2 + - - +
305B GLU* 3.6 15.2 + - - +
307B ALA* 1.3 74.9 - - - +
309B TRP* 1.3 66.7 + - - +
311B ASN* 3.3 11.8 + - + +
312B ASP* 3.0 26.6 + - - +
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Residues in contact with TRP 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B VAL* 3.8 16.6 - - + -
155B PRO* 3.5 24.0 - - + -
156B SER* 3.5 37.2 - - - -
157B ILE* 4.1 10.1 - - + -
305B GLU 2.8 19.0 + - - +
306B GLY* 3.5 4.3 - - - +
308B LYS* 1.3 75.8 - - - +
310B LEU* 1.3 59.2 + - - +
312B ASP* 2.9 30.9 + - + +
313B LEU 3.1 8.5 + - - -
318B LYS* 2.9 36.5 + - + +
319B ILE* 3.7 40.5 - - + +
320B TYR* 4.2 11.2 - + + -
322B GLY 5.1 1.1 - - - -
324B ARG* 3.7 42.8 - - + +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 4.0 19.3 - - + -
119B GLY 3.8 5.8 - - - -
120B VAL 3.7 18.6 - - - +
121B LEU* 3.5 30.3 - - + -
140B PRO 3.6 27.4 - - - +
142B VAL* 3.6 23.7 - - + +
306B GLY 2.7 21.0 + - - +
307B ALA 3.4 4.5 - - - +
309B TRP* 1.3 71.3 - - - +
311B ASN* 1.3 66.1 + - - +
313B LEU* 2.9 9.2 + - + +
314B ILE* 2.9 39.4 + - + +
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Residues in contact with ASN 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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62B PHE* 3.8 7.1 - - + -
85B TRP* 3.4 35.3 - - + -
89B ASN* 5.2 3.8 - - - +
91B LYS* 3.5 27.6 + - - +
307B ALA 2.9 6.1 + - - -
308B LYS* 3.4 10.3 - - - +
309B TRP 3.2 0.4 - - - -
310B LEU* 1.3 76.4 - - - +
312B ASP* 1.3 60.7 + - - +
314B ILE* 3.2 27.2 - - - +
315B ALA* 3.3 9.0 + - - +
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Residues in contact with ASP 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LYS* 3.0 29.1 + - - +
309B TRP* 2.9 20.0 + - + +
311B ASN* 1.3 79.6 + - - +
313B LEU* 1.3 54.4 + - - +
314B ILE 3.0 2.0 - - - -
315B ALA* 3.0 8.2 + - - +
316B GLY 2.7 31.4 + - - -
317B GLU* 3.4 27.4 + - + +
318B LYS* 4.5 12.1 - - - +
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Residues in contact with LEU 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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140B PRO* 3.6 22.3 - - + +
141B THR 3.4 42.8 - - - +
142B VAL* 4.2 3.1 - - + -
154B LEU* 6.3 0.2 - - + -
155B PRO* 4.4 5.6 - - + -
309B TRP 3.1 4.9 + - - -
310B LEU* 2.9 13.1 + - + +
312B ASP* 1.3 76.3 - - - +
314B ILE* 1.3 64.2 + - - +
316B GLY* 3.0 12.8 + - - +
317B GLU 4.6 0.2 - - - +
318B LYS* 3.2 44.8 - - + +
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Residues in contact with ILE 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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62B PHE* 3.7 15.7 - - + -
91B LYS* 5.9 3.4 - - - +
118B ASP* 3.5 42.4 - - + +
119B GLY* 3.6 16.6 - - - -
140B PRO* 3.9 10.7 - - + +
310B LEU* 2.9 31.0 + - + +
311B ASN* 3.2 21.3 - - - +
313B LEU* 1.3 79.8 - - - +
315B ALA* 1.3 61.7 + - - +
316B GLY* 3.2 0.5 + - - -
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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
----------------------------------------------------------
311B ASN 3.3 9.3 + - - +
312B ASP* 3.0 7.9 + - - +
314B ILE* 1.3 80.7 - - - +
316B GLY* 1.3 63.2 + - - +
317B GLU* 4.0 16.2 - - - +
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Residues in contact with GLY 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASP 2.7 10.3 + - - -
313B LEU* 3.0 15.6 + - - -
314B ILE 3.1 1.0 - - - -
315B ALA* 1.3 75.1 - - - +
317B GLU* 1.3 69.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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