Contacts of the helix formed by residues 305 - 321 (chain B) in PDB entry 4IVR
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 TYR 305 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 5.7 0.2 - - - +
91A LEU* 3.3 43.9 - - + +
371A GLU* 3.4 23.8 - - + +
296B GLU 4.7 4.5 - - - -
297B LEU 3.2 27.8 + - - -
298B LEU 3.3 21.4 + - - -
299B ALA* 3.5 28.6 - - + -
300B PRO* 3.8 9.9 - - + +
303B ASP 3.4 1.2 + - - -
304B LEU* 1.3 75.2 - - - +
306B ASN* 1.3 66.7 + - - +
307B VAL* 4.2 3.8 - - + -
308B PHE* 3.2 27.2 + + + -
309B ALA* 3.1 17.2 + - - +
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Residues in contact with ASN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A THR* 3.4 25.1 + - + +
371A GLU* 2.8 35.1 + - + +
256B ARG* 5.4 5.4 + - - -
304B LEU 4.4 3.1 + - - +
305B TYR* 1.3 71.4 - - - +
307B VAL* 1.3 55.5 + - - +
309B ALA* 3.4 10.4 - - - +
310B TRP* 2.9 60.3 + - + -
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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
----------------------------------------------------------
87A TYR* 3.9 22.0 - - + -
91A LEU* 5.2 3.1 - - + -
130A MET* 3.5 31.9 - - - +
131A PRO* 4.3 4.5 - - + -
134A VAL* 4.0 12.7 - - + +
371A GLU* 3.0 12.1 + - - +
372A MET* 3.5 31.9 - - + -
305B TYR* 4.2 2.9 - - + -
306B ASN* 1.3 78.1 - - - +
308B PHE* 1.3 84.1 + - + +
310B TRP* 3.5 14.0 + - + +
311B ALA 3.4 13.9 + - - -
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Residues in contact with PHE 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TYR* 3.6 34.8 - + - -
91A LEU* 3.9 11.2 - - + -
130A MET* 4.1 8.5 - - + -
185B GLN* 3.8 20.6 - - + -
188B LEU* 3.7 22.0 - - + +
296B GLU 4.3 2.2 - - - -
297B LEU* 3.5 57.2 - - + -
304B LEU* 4.1 13.0 - - + -
305B TYR* 3.2 26.3 + + + +
307B VAL* 1.3 77.2 - - + +
309B ALA* 1.3 67.6 + - - +
310B TRP 3.2 1.8 - - - -
311B ALA* 3.1 7.3 + - - +
312B LEU* 3.0 26.3 + - + +
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B TRP* 3.4 31.4 - - + -
256B ARG* 3.6 22.2 - - - +
304B LEU* 4.3 11.4 - - + +
305B TYR 3.1 13.0 + - - +
306B ASN* 3.4 16.2 - - - +
308B PHE* 1.3 77.7 - - - +
310B TRP* 1.3 56.6 + - - +
312B LEU 3.2 2.1 + - - -
313B ASP* 3.0 23.9 + - - +
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Residues in contact with TRP 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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134A VAL* 4.3 14.6 - - + -
135A THR* 5.6 2.5 - - - -
138A VAL* 3.9 29.8 - - + +
363A ASP* 6.0 0.2 - - - -
364A LEU* 4.0 18.9 - - + +
367A THR* 3.5 36.8 - - + -
368A PHE* 3.6 41.5 - + + -
372A MET* 3.9 5.4 - - + -
256B ARG* 4.2 8.6 - - - +
306B ASN* 2.9 40.2 + - + +
307B VAL* 3.5 15.9 - - + +
308B PHE 3.2 0.2 - - - -
309B ALA* 1.3 72.7 - - - +
311B ALA* 1.3 65.8 + - - +
313B ASP* 3.0 21.6 + - - +
314B VAL* 2.9 26.9 + - - +
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Residues in contact with ALA 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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130A MET* 4.0 15.9 - - + -
134A VAL* 3.8 22.2 - - + +
188B LEU* 4.0 28.0 - - + +
191B VAL* 3.5 12.2 - - + +
192B ALA* 5.1 0.4 - - + -
307B VAL 3.4 3.4 + - - -
308B PHE 3.1 10.0 + - - +
310B TRP* 1.3 78.1 - - - +
312B LEU* 1.3 57.4 + - - +
314B VAL* 3.2 7.6 + - - +
315B LEU* 2.9 23.7 + - - +
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Residues in contact with LEU 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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188B LEU* 4.1 14.1 - - + -
255B TRP* 3.6 28.1 + - + +
259B TRP* 4.2 9.0 - - + -
289B PHE* 3.8 23.7 - - + +
292B PHE* 3.7 40.8 - - + -
304B LEU* 3.6 26.9 - - + -
308B PHE 3.0 16.0 + - - +
309B ALA 3.2 8.3 + - - +
311B ALA* 1.3 74.2 - - - +
313B ASP* 1.3 59.0 + - - +
315B LEU* 3.5 9.4 + - + +
316B ALA* 3.0 26.7 + - - +
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.6 9.9 - - + +
255B TRP* 2.8 24.9 + - - +
256B ARG* 2.9 33.1 + - - -
309B ALA 3.0 8.9 + - - +
310B TRP* 3.0 19.6 + - - +
312B LEU* 1.3 73.9 - - - +
314B VAL* 1.3 60.7 + - - +
316B ALA* 3.4 6.0 + - - +
317B LYS* 2.9 29.1 + - - +
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Residues in contact with VAL 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A VAL* 4.7 6.5 - - + +
137A ALA* 3.7 27.1 - - + -
138A VAL* 4.3 10.8 - - + -
191B VAL* 3.8 22.4 - - + +
192B ALA* 4.5 7.0 - - - +
194B ILE 5.2 0.2 - - - +
310B TRP 2.9 20.6 + - - +
311B ALA* 3.4 11.9 - - - +
313B ASP* 1.3 74.2 - - - +
315B LEU* 1.3 66.7 + - - +
317B LYS* 3.2 5.8 + - - +
318B ARG* 2.9 57.3 + - + +
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Residues in contact with LEU 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LEU* 3.7 28.5 - - + -
191B VAL* 4.0 16.8 - - + -
194B ILE* 4.5 6.5 - - + -
245B THR* 5.2 0.4 - - + -
288B LEU* 4.5 15.7 - - + -
289B PHE* 4.1 23.1 - - + -
292B PHE* 4.4 22.9 - - + -
311B ALA 2.9 15.8 + - - +
312B LEU* 3.6 9.6 - - + +
314B VAL* 1.3 75.7 - - - +
316B ALA* 1.3 64.1 + - - +
318B ARG* 3.3 3.7 + - - +
319B LEU* 3.0 57.8 + - + +
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Residues in contact with ALA 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LEU* 3.6 28.2 - - + +
255B TRP* 4.6 7.2 - - + -
289B PHE* 4.2 9.1 - - + -
312B LEU 3.0 15.6 + - - +
313B ASP* 3.4 11.2 - - - +
315B LEU* 1.3 76.2 - - - +
317B LYS* 1.3 62.0 + - - +
320B ARG* 3.1 29.9 + - - +
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Residues in contact with LYS 317 (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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141A PRO* 4.1 25.4 - - + +
197B THR* 4.6 0.5 + - - -
313B ASP 2.9 20.1 + - - +
314B VAL* 3.7 5.8 - - - +
316B ALA* 1.3 73.4 - - - +
318B ARG* 1.3 85.1 + - - +
320B ARG* 3.7 35.3 + - - +
321B SER* 3.9 15.7 + - - -
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Residues in contact with ARG 318 (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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137A ALA* 4.0 29.1 + - - +
192B ALA 5.2 1.4 + - - -
194B ILE* 2.9 45.4 + - + -
195B PRO 3.2 19.0 + - - -
196B PRO* 3.9 28.3 - - - +
197B THR* 2.7 32.5 + - - +
314B VAL* 2.9 36.1 + - + +
315B LEU* 3.8 5.2 - - - +
317B LYS* 1.3 102.7 - - - +
319B LEU* 1.3 70.3 + - + +
320B ARG 3.6 0.2 + - - -
321B SER 3.9 1.6 + - - -
322B MET* 3.9 8.2 - - + +
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Residues in contact with LEU 319 (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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166B ILE* 4.3 11.2 - - + -
170B LEU* 4.5 6.3 - - + -
194B ILE* 5.8 0.2 - - + -
242B LEU* 3.7 31.4 - - + -
245B THR* 3.7 26.5 - - + -
246B VAL* 3.5 25.3 - - + +
249B LEU* 3.7 10.3 - - + -
288B LEU* 4.2 4.0 - - + -
315B LEU* 3.0 42.2 + - + +
318B ARG* 1.3 78.8 - - + +
320B ARG* 1.3 67.0 + - - +
322B MET* 3.1 35.0 + - + +
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Residues in contact with ARG 320 (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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246B VAL 5.1 0.2 - - - -
249B LEU* 3.8 44.4 - - + +
250B GLN* 2.9 32.2 + - + +
316B ALA 3.1 18.7 + - - +
317B LYS* 3.7 36.9 + - - +
318B ARG 3.4 0.6 - - - -
319B LEU* 1.3 77.8 - - - +
321B SER* 1.3 61.6 + - - +
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Residues in contact with SER 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B THR* 3.5 33.0 + - - +
198B LEU 5.2 0.9 - - - +
201B THR* 4.7 1.4 + - - +
250B GLN* 4.7 0.9 - - - +
317B LYS* 3.9 12.4 + - - -
318B ARG 3.9 0.6 + - - -
319B LEU 3.2 0.6 - - - -
320B ARG* 1.3 81.3 - - - +
322B MET* 1.3 63.7 + - - +
323B HIS* 3.6 20.7 + - - -
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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
------------------------------------------------------------
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