Contacts of the helix formed by residues 299 - 317 (chain B) in PDB entry 4R1Z
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 THR 299 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS* 5.2 0.2 - - - -
283B LYS* 4.0 5.8 - - - +
297B GLY* 5.3 1.1 - - - -
298B LEU* 1.3 85.0 - - - +
300B GLU* 1.3 65.7 + - - +
301B ASP* 3.5 15.5 + - - +
302B HIS* 2.7 44.2 + - + +
303B VAL* 3.0 10.2 + - - +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLN* 4.9 7.2 + - - +
260B TYR* 3.0 45.0 + - + +
264B LYS* 4.2 7.4 + - - -
283B LYS* 3.6 18.4 + - - +
299B THR* 1.3 72.1 - - - +
301B ASP* 1.3 63.7 + - - +
303B VAL* 3.3 5.4 + - - +
304B LEU* 3.1 42.2 + - + +
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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
----------------------------------------------------------
120B ARG* 2.7 40.8 + - - +
123B LYS* 3.9 25.5 + - + -
299B THR* 2.9 12.1 + - - +
300B GLU* 1.3 79.8 - - - +
302B HIS* 1.3 61.7 + - - +
304B LEU* 4.1 0.5 - - - +
305B MET* 3.2 30.9 + - - +
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Residues in contact with HIS 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS* 3.2 43.9 - - + +
124B ASP 4.5 1.9 + - - +
133B THR* 3.8 17.9 - - + +
137B HIS* 3.5 19.7 - + + +
297B GLY* 3.5 35.9 - - - -
298B LEU 4.1 1.1 - - - -
299B THR* 2.7 47.7 + - + +
301B ASP* 1.3 72.8 - - - +
303B VAL* 1.3 63.4 + - - +
305B MET* 3.3 3.1 + - - +
306B THR* 3.1 28.8 + - - -
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Residues in contact with VAL 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B HIS* 4.8 3.6 - - - +
260B TYR* 4.2 15.0 - - + -
276B LEU* 4.2 17.3 - - + -
279B LEU* 3.9 37.8 - - + +
280B LEU* 5.0 2.7 - - + -
283B LYS* 4.2 13.9 - - + -
298B LEU* 3.4 27.1 - - + +
299B THR 3.0 15.3 + - - +
300B GLU* 3.7 8.3 - - - +
301B ASP 3.3 0.2 - - - -
302B HIS* 1.3 77.2 - - + +
304B LEU* 1.3 62.7 + - - +
306B THR* 4.9 0.2 - - - -
307B VAL* 3.2 23.4 + - - +
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Residues in contact with LEU 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B ARG* 4.2 20.0 - - - +
256B LEU* 3.4 40.1 - - + +
257B GLN* 3.5 23.3 - - - +
260B TYR* 3.7 36.3 - - + -
276B LEU* 5.5 4.0 - - + -
300B GLU* 3.1 40.1 + - + +
301B ASP 4.2 1.8 - - - +
303B VAL* 1.3 74.8 - - - +
305B MET* 1.3 63.3 + - - +
307B VAL* 3.6 5.3 + - + +
308B GLY 3.0 22.2 + - - -
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Residues in contact with MET 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU 3.2 20.6 - - - +
119B THR* 3.3 26.5 - - - +
120B ARG* 3.6 35.2 - - + -
123B LYS* 4.0 0.9 - - + -
124B ASP* 3.3 27.6 - - + +
252B ARG* 3.2 32.8 - - - +
253B ASP* 5.1 0.2 - - - +
256B LEU* 4.9 2.0 - - + -
301B ASP 3.2 18.6 + - - +
302B HIS 3.3 1.3 + - - +
304B LEU* 1.3 81.4 - - - +
306B THR* 1.3 60.2 + - - +
308B GLY* 3.3 2.1 + - - -
309B ASP* 2.9 34.6 + - - +
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Residues in contact with THR 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 4.1 12.4 - - - +
125B ILE* 3.9 13.0 - - + +
137B HIS* 3.1 36.3 - - + +
141B VAL* 3.9 27.1 - - + -
275B LEU* 5.2 0.7 - - + -
279B LEU* 4.1 15.7 - - + -
302B HIS 3.1 10.4 + - - -
303B VAL 4.0 4.9 - - - -
305B MET* 1.3 76.8 - - - +
307B VAL* 1.3 64.1 + - - +
309B ASP* 3.3 8.2 + - - +
310B ILE* 3.2 21.9 + - + +
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Residues in contact with VAL 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B CYS* 4.0 16.6 - - + +
197B PHE* 3.4 37.0 - - + -
256B LEU* 5.2 2.9 - - + -
275B LEU* 4.3 12.8 - - + -
276B LEU* 3.9 21.8 - - + -
279B LEU* 3.7 20.0 - - + -
303B VAL 3.2 19.2 + - - +
304B LEU* 3.9 5.8 - - + +
305B MET 3.4 0.2 - - - -
306B THR* 1.3 75.5 - - - +
308B GLY* 1.3 52.9 + - - +
310B ILE* 3.4 2.1 + - - +
311B PHE* 2.7 37.9 + - - +
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Residues in contact with GLY 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ARG* 4.8 13.5 - - - -
256B LEU* 4.3 16.0 - - - +
304B LEU 3.0 14.9 + - - -
305B MET 3.3 4.7 + - - -
306B THR 3.3 0.2 - - - -
307B VAL* 1.3 72.3 - - - +
309B ASP* 1.3 55.5 + - - +
311B PHE* 3.1 5.1 + - - -
312B GLY* 2.6 35.3 + - - -
601B AER 4.2 8.3 - - - +
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Residues in contact with ASP 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ASP* 2.8 32.8 - - - +
125B ILE* 2.7 32.1 + - + +
126B ALA* 2.9 11.2 + - - -
305B MET* 2.9 12.0 + - - +
306B THR* 3.3 10.7 + - - +
308B GLY* 1.3 70.5 - - - +
310B ILE* 1.3 63.8 + - + +
313B ALA* 2.9 34.6 + - - +
600B HEM 4.8 6.9 - - + +
601B AER 3.9 28.7 - - + +
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Residues in contact with ILE 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ILE* 5.0 1.1 - - + -
141B VAL* 3.7 32.1 - - + -
192B VAL* 3.6 10.0 - - + +
195B LEU* 4.7 9.0 - - + -
196B CYS* 3.7 20.9 - - - -
275B LEU* 4.0 17.5 - - + -
306B THR 3.2 14.6 + - - +
307B VAL 3.7 4.7 - - - +
309B ASP* 1.3 75.3 - - + +
311B PHE* 1.3 61.6 + - - +
313B ALA* 3.9 0.2 - - - +
314B GLY* 2.8 32.7 + - - -
454B LEU* 4.1 12.6 - - + -
458B LEU* 5.8 2.0 - - + -
600B HEM 3.7 32.5 - - + +
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Residues in contact with PHE 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B THR* 3.9 18.6 - - + -
192B VAL* 4.1 22.7 - - + +
193B CYS* 4.3 11.4 - - + -
196B CYS* 4.4 3.1 - - - -
197B PHE* 3.6 37.9 - + + -
201B TYR* 4.3 12.1 - + - -
211B MET* 3.6 44.2 - - + -
214B TYR* 4.3 9.2 - - - -
252B ARG* 6.2 1.6 - - + -
255B LEU* 4.9 6.7 - - + -
256B LEU* 5.0 7.4 - - + -
307B VAL 2.7 24.7 + - - +
308B GLY* 3.9 4.5 - - - +
310B ILE* 1.3 74.1 - - - +
312B GLY* 1.3 62.3 + - - +
315B VAL* 3.3 24.1 + - + +
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Residues in contact with GLY 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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308B GLY 2.6 19.4 + - - -
311B PHE* 1.3 72.8 - - - +
313B ALA* 1.3 65.4 + - - +
314B GLY 3.1 0.9 - - - -
315B VAL* 2.9 17.0 + - - +
316B GLU* 3.0 13.7 + - - +
601B AER 3.9 35.2 - - - +
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Residues in contact with ALA 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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309B ASP 2.9 22.4 + - - +
310B ILE 3.9 1.1 - - - +
312B GLY* 1.3 70.3 - - - -
314B GLY* 1.3 58.0 + - - +
317B THR* 2.8 37.7 + - + -
600B HEM 3.8 33.0 - - + -
601B AER 3.7 37.0 - - + +
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Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B VAL* 3.0 25.6 - - - +
192B VAL* 4.0 21.3 - - - +
310B ILE 2.8 22.6 + - - -
313B ALA* 1.3 73.1 - - - +
315B VAL* 1.3 58.9 + - - +
318B THR* 3.7 6.3 + - - -
458B LEU* 6.5 0.2 - - - -
462B GLU* 4.8 1.9 - - - +
600B HEM 3.9 18.1 - - - +
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B THR* 4.7 10.8 - - + +
188B VAL* 4.4 3.4 - - - -
189B THR* 3.5 37.7 - - + +
192B VAL* 4.3 3.1 - - + -
211B MET* 4.4 18.8 - - + -
212B LEU* 5.6 7.0 - - + -
215B SER* 6.1 1.3 - - - +
311B PHE* 3.3 18.4 + - + +
312B GLY* 2.9 7.5 + - - +
314B GLY* 1.3 78.5 - - - +
316B GLU* 1.3 76.9 + - + +
317B THR 3.4 1.1 + - - -
319B THR* 2.5 35.4 + - - +
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Residues in contact with GLU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B SER* 3.9 14.4 - - - -
216B GLN 5.9 0.2 - - - -
219B VAL* 3.9 19.2 - - + +
312B GLY 3.0 14.5 + - - +
313B ALA 4.2 0.7 - - - +
315B VAL* 1.3 89.7 - - - +
317B THR* 1.3 54.6 + - - +
319B THR* 5.0 0.6 - - - -
320B THR* 2.5 30.1 + - - -
493B VAL* 4.7 7.2 - - + -
494B VAL* 3.7 13.3 - - + +
496B GLN* 5.3 4.8 - - - +
601B AER 3.4 45.7 - - + +
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Residues in contact with THR 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ALA* 2.8 20.9 + - - +
316B GLU* 1.3 76.6 - - - +
318B THR* 1.3 75.5 + - - +
319B THR 3.2 1.1 - - - -
320B THR* 2.9 15.8 + - - -
321B VAL* 3.0 15.1 + - - +
377B VAL* 4.1 11.2 - - + +
494B VAL* 4.2 3.6 - - + -
600B HEM 3.0 38.9 - - + +
601B AER 3.4 46.9 - - + +
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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
------------------------------------------------------------
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