Contacts of the helix formed by residues 305 - 320 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A GLU 4.4 7.0 - - - -
297A LEU 3.2 29.2 + - - -
298A LEU 3.4 19.4 + - - -
299A ALA* 3.4 28.5 - - + +
300A PRO* 3.9 10.6 - - + +
303A ASP 3.6 1.4 + - - -
304A LEU* 1.3 73.7 - - - +
306A ASN* 1.3 66.0 + - - +
307A VAL* 3.2 4.0 - - + +
308A PHE* 3.1 36.2 + + + +
309A ALA 3.1 9.2 + - - -
91B LEU* 3.8 33.2 - - + +
371B GLU* 3.7 26.9 - - + +
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Residues in contact with ASN 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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256A ARG* 5.6 3.1 + - - -
304A LEU 3.4 4.4 + - - -
305A TYR* 1.3 71.6 - - - +
307A VAL* 1.3 56.3 + - - +
309A ALA* 3.2 10.3 + - - +
310A TRP* 2.9 47.9 + - + +
367B THR* 3.4 34.1 - - + +
371B GLU* 2.8 34.8 + - - +
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Residues in contact with VAL 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A TYR* 4.4 2.5 - - + -
306A ASN* 1.3 76.2 - - - +
308A PHE* 1.3 80.2 + - + +
310A TRP* 3.6 12.3 + - - +
311A ALA* 3.4 14.9 + - - +
87B TYR* 3.6 25.8 - - + -
91B LEU* 5.1 2.7 - - + -
130B MET* 3.6 30.5 - - - +
131B PRO* 4.5 1.8 - - + -
134B VAL* 3.8 17.5 - - + +
371B GLU* 3.0 12.1 + - - +
372B MET* 3.8 31.9 - - + -
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Residues in contact with PHE 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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185A GLN* 3.6 29.8 - - + -
188A LEU* 3.8 23.9 - - + +
296A GLU 4.3 2.7 - - - -
297A LEU* 3.6 38.4 - - + -
304A LEU* 4.1 13.5 - - + -
305A TYR* 3.1 31.5 + + + +
307A VAL* 1.3 78.3 - - + +
309A ALA* 1.3 64.7 + - - +
311A ALA* 3.0 6.3 + - - +
312A LEU* 3.0 26.5 + - + +
87B TYR* 3.5 38.4 - + - -
91B LEU* 3.9 11.2 - - + -
130B MET* 3.7 12.8 - - + -
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Residues in contact with ALA 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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255A TRP* 3.4 28.3 - - + -
256A ARG* 3.7 18.6 - - - +
304A LEU* 4.1 12.0 - - + +
305A TYR 3.1 11.2 + - - +
306A ASN* 3.5 15.5 - - - +
308A PHE* 1.3 76.5 - - - +
310A TRP* 1.3 57.6 + - + +
312A LEU* 3.1 5.8 + - - +
313A ASP* 2.9 29.1 + - - -
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Residues in contact with TRP 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ARG* 3.9 9.3 - - - +
306A ASN* 2.9 27.7 + - + +
307A VAL* 3.7 15.3 - - + +
308A PHE 3.2 0.2 - - - -
309A ALA* 1.3 75.7 - - - +
311A ALA* 1.3 58.2 + - - +
313A ASP* 3.2 21.5 + - - +
314A VAL* 3.0 29.5 + - - +
134B VAL* 4.6 18.8 - - + -
135B THR* 5.3 0.9 - - - -
138B VAL* 3.8 20.2 - - + +
363B ASP* 5.9 0.9 - - - -
364B LEU* 3.4 44.3 - - + +
367B THR* 3.8 25.4 - - + -
368B PHE* 3.7 44.6 - + - -
371B GLU* 5.4 0.4 - - + -
372B MET* 4.3 10.5 - - + -
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Residues in contact with ALA 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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188A LEU* 4.1 35.9 - - + +
191A VAL* 3.3 15.6 - - + +
192A ALA* 4.8 1.8 - - + -
307A VAL 3.4 9.8 + - - +
308A PHE* 3.0 10.8 + - - +
310A TRP* 1.3 76.0 - - - +
312A LEU* 1.3 61.6 + - - +
314A VAL* 3.3 9.6 + - - +
315A LEU* 3.0 22.3 + - - +
130B MET* 4.5 1.3 - - + -
134B VAL* 4.3 13.4 - - + +
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Residues in contact with LEU 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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188A LEU* 4.0 16.6 - - + -
255A TRP* 3.7 26.2 - - + +
259A TRP* 4.0 12.8 - - + -
289A PHE* 3.8 25.2 - - + -
292A PHE* 3.6 38.6 - - + -
304A LEU* 3.6 27.6 - - + -
308A PHE 3.0 15.7 + - - +
309A ALA 3.1 8.3 + - - +
311A ALA* 1.3 74.9 - - - +
313A ASP* 1.3 63.8 + - - +
315A LEU* 3.1 10.9 + - + +
316A ALA* 3.0 19.2 + - - +
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Residues in contact with ASP 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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255A TRP* 2.8 24.8 + - - +
256A ARG* 2.7 35.9 + - - -
309A ALA 2.9 14.4 + - - +
310A TRP* 3.2 19.7 + - - +
312A LEU* 1.3 76.8 - - - +
314A VAL* 1.3 57.2 + - - +
316A ALA* 3.2 6.2 + - - +
317A LYS* 2.9 29.4 + - - +
138B VAL* 4.7 8.7 - - + +
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 3.9 20.9 - - + +
192A ALA* 4.4 9.6 - - - +
194A ILE 5.1 0.2 - - - +
310A TRP 3.0 16.0 + - - +
311A ALA* 3.5 12.1 - - - +
312A LEU 3.2 0.2 - - - -
313A ASP* 1.3 74.3 - - - +
315A LEU* 1.3 63.6 + - - +
317A LYS* 3.2 7.0 + - - +
318A ARG* 2.9 54.1 + - + +
134B VAL* 4.6 3.8 - - - +
137B ALA* 3.7 30.1 - - + -
138B VAL* 4.1 12.1 - - + +
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Residues in contact with LEU 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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170A LEU* 4.0 26.9 - - + -
191A VAL* 4.0 15.5 - - + +
194A ILE* 4.7 6.3 - - + -
245A THR* 5.2 0.4 - - + -
288A LEU* 4.3 19.7 - - + -
289A PHE* 3.8 27.4 - - + -
292A PHE* 4.4 9.2 - - + -
311A ALA 3.0 13.0 + - - +
312A LEU* 3.2 18.6 - - + +
314A VAL* 1.3 76.6 - - - +
316A ALA* 1.3 57.9 + - - +
318A ARG* 3.2 5.7 + - - +
319A LEU* 2.9 62.3 + - + +
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Residues in contact with ALA 316 (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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249A LEU* 3.7 31.9 - - + -
255A TRP* 4.6 8.7 - - + -
289A PHE* 4.0 10.5 - - + -
312A LEU 3.0 12.6 + - - +
313A ASP* 3.2 8.0 + - - +
315A LEU* 1.3 74.9 - - - +
317A LYS* 1.3 63.8 + - - +
320A ARG* 3.0 34.0 + - + +
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Residues in contact with LYS 317 (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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197A THR* 4.7 1.0 + - - -
313A ASP 2.9 16.4 + - - +
314A VAL* 3.6 7.6 - - - +
316A ALA* 1.3 77.2 - - - +
318A ARG* 1.3 82.6 + - - +
320A ARG* 3.3 52.6 + - - +
321A SER* 4.4 7.9 + - - -
141B PRO* 3.7 31.4 - - + +
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Residues in contact with ARG 318 (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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192A ALA 5.5 0.6 + - - -
194A ILE* 3.0 48.6 + - + -
195A PRO 3.1 20.9 + - - -
196A PRO* 3.8 27.4 - - - +
197A THR* 2.7 32.4 + - - +
314A VAL* 2.9 38.6 + - + +
315A LEU* 3.7 5.2 - - - +
317A LYS* 1.3 106.0 - - - +
319A LEU* 1.3 68.8 + - + +
321A SER* 4.1 1.7 + - - -
322A MET* 3.7 10.5 - - + +
137B ALA* 4.4 21.0 + - - +
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Residues in contact with LEU 319 (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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166A ILE* 4.6 11.4 - - + -
170A LEU* 4.5 2.2 - - + -
194A ILE* 5.7 0.7 - - + -
242A LEU* 3.7 31.2 - - + -
245A THR* 3.7 23.8 - - + -
246A VAL* 3.8 16.5 - - + +
249A LEU* 3.7 11.7 - - + -
288A LEU* 3.8 4.9 - - + -
315A LEU* 2.9 42.4 + - + +
318A ARG* 1.3 77.9 - - + +
320A ARG* 1.3 60.1 + - - +
321A SER 3.1 2.7 - - - -
322A MET* 2.9 54.4 + - + +
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Residues in contact with ARG 320 (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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246A VAL 5.1 1.1 - - - -
249A LEU* 3.7 33.6 - - + +
250A GLN* 3.0 29.7 + - - +
316A ALA* 3.0 21.9 + - - +
317A LYS* 3.3 50.6 + - - +
319A LEU* 1.3 76.5 - - - +
321A SER* 1.3 64.3 + - - +
322A MET 3.3 0.7 - - - -
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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
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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