Contacts of the helix formed by residues 334 - 354 (chain B) in PDB entry 4R0C
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 MET 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B VAL* 3.7 29.8 - - + -
87B LEU* 3.9 16.8 - - + -
90B MET* 3.7 28.7 - - + -
330B THR* 3.3 17.0 - - - +
331B MET* 3.1 29.6 + - + +
333B SER* 1.3 78.0 - - - +
335B ALA* 1.3 63.5 + - - +
336B GLY 3.3 1.1 - - - -
337B TYR* 3.0 29.3 + - + +
338B LEU* 3.0 25.3 + - + +
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLU* 3.2 33.4 - - + +
331A MET* 4.1 8.9 - - + +
332A ALA* 3.8 14.1 - - + +
331B MET 3.8 2.7 + - - -
332B ALA 3.2 16.6 + - - +
333B SER 3.1 3.2 - - - +
334B MET* 1.3 77.1 - - - +
336B GLY* 1.3 64.0 + - - +
338B LEU* 3.2 7.1 + - - +
339B VAL* 3.1 25.1 + - - +
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Residues in contact with GLY 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A GLU* 3.7 27.7 + - - +
20B HIS* 5.9 0.6 - - - -
22B THR* 4.4 4.2 + - - -
333B SER 4.3 3.6 + - - -
334B MET 3.3 0.6 - - - -
335B ALA* 1.3 79.1 - - - +
337B TYR* 1.3 61.1 + - - +
339B VAL* 3.5 2.3 + - - +
340B LEU* 3.0 23.3 + - - +
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Residues in contact with TYR 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 2.9 28.4 + - - +
83B LEU* 4.2 12.6 - - + -
86B VAL* 3.4 19.4 - - + +
87B LEU* 4.8 3.8 - - + -
182B THR* 2.6 31.7 + - + -
333B SER 5.4 0.4 + - - -
334B MET* 3.0 33.3 + - + +
336B GLY* 1.3 72.2 - - - +
338B LEU* 1.3 57.6 + - - +
340B LEU* 2.9 9.1 + - + +
341B MET* 2.6 65.7 + - + +
397B SER* 3.7 22.7 - - - -
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Residues in contact with LEU 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A LEU* 5.1 6.5 - - + -
91A LEU* 5.9 0.4 - - - +
331A MET* 4.3 32.5 - - + +
338A LEU* 3.9 28.3 - - + -
77B PHE* 3.6 22.0 - - + -
83B LEU* 3.7 24.9 - - + -
87B LEU* 3.7 24.7 - - + -
331B MET 5.2 2.5 - - - +
334B MET* 3.0 20.5 + - + +
335B ALA* 3.4 10.1 - - - +
337B TYR* 1.3 75.9 - - - +
339B VAL* 1.3 62.7 + - - +
341B MET* 3.6 3.3 + - - -
342B PHE* 3.0 22.5 + - - +
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Residues in contact with VAL 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.8 13.9 - - + -
324A ILE* 4.6 6.1 - - + -
327A MET* 3.4 46.7 - - + +
328A GLU* 4.0 7.4 - - + +
331A MET* 3.7 27.1 - - + -
22B THR* 3.8 14.1 - - + -
335B ALA 3.1 12.6 + - - +
336B GLY 4.1 3.4 - - - +
337B TYR 3.2 0.2 - - - -
338B LEU* 1.3 75.2 - - - +
340B LEU* 1.3 63.3 + - - +
342B PHE* 3.3 12.4 + - - +
343B PHE* 3.4 20.6 + - + -
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PRO* 5.3 0.7 - - + -
22B THR* 3.5 30.7 - - + +
25B PHE* 3.7 37.7 - - + -
336B GLY 3.0 14.2 + - - +
337B TYR* 2.9 12.9 + - + +
339B VAL* 1.3 78.6 - - - +
341B MET* 1.3 78.9 + - + +
342B PHE 3.4 0.2 + - - -
343B PHE* 3.5 1.6 + - - +
344B ALA* 2.9 33.0 + - + +
395B SER* 5.2 0.9 - - - +
397B SER* 3.8 22.4 - - - -
398B ALA* 4.0 16.8 - - + +
401B SER* 4.8 0.4 - - - +
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Residues in contact with MET 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.1 4.0 - - + -
80B PHE* 3.7 8.9 - - + -
82B PRO* 3.7 31.0 - - + -
83B LEU* 3.8 20.6 - - + -
182B THR* 5.5 0.7 - - + -
186B LEU* 4.6 4.0 - - + -
337B TYR* 2.6 60.2 + - + +
338B LEU 4.0 2.2 - - - +
340B LEU* 1.3 102.7 - - + +
342B PHE* 1.3 60.0 + - - +
344B ALA* 4.3 4.7 - - + -
345B ALA* 2.8 33.3 + - - +
397B SER* 4.6 4.0 - - - -
401B SER* 3.8 17.7 - - - +
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Residues in contact with PHE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.6 38.4 - - + -
91A LEU* 3.5 29.4 - - + -
806A LMT 4.1 12.3 - - + -
73B LEU* 4.0 16.2 - - + -
77B PHE* 3.4 35.3 - + + -
338B LEU 3.0 14.8 + - - +
339B VAL 3.5 9.4 - - - +
340B LEU 3.2 0.4 - - - -
341B MET* 1.3 80.2 - - - +
343B PHE* 1.3 88.2 + + - +
345B ALA* 3.5 2.8 - - - +
346B GLN* 3.1 50.9 + - + +
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Residues in contact with PHE 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.7 0.4 - - + -
327A MET* 3.4 38.8 - - + -
806A LMT 4.6 17.7 - - + -
22B THR* 4.3 6.3 - - + +
25B PHE* 3.8 22.6 - - + +
26B VAL* 3.5 36.1 - - + -
29B CYS* 3.5 20.3 - - + -
339B VAL* 3.4 20.9 + - + -
340B LEU 4.2 2.9 - - - +
342B PHE* 1.3 100.2 - + - +
344B ALA* 1.3 60.5 + - - +
346B GLN* 3.2 3.8 + - + +
347B PHE* 2.9 25.6 + - - +
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Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 3.7 20.5 - - + -
80B PHE* 3.9 11.9 - - + -
340B LEU* 2.9 22.5 + - + +
341B MET* 4.1 5.2 - - + +
343B PHE* 1.3 75.6 - - - +
345B ALA* 1.3 63.1 + - - +
347B PHE* 3.3 1.6 + - - +
348B VAL* 3.1 30.3 + - + +
401B SER* 3.9 29.8 - - - +
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Residues in contact with ALA 345 (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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76B ASN* 3.6 21.7 - - - +
77B PHE* 4.2 5.2 - - - -
80B PHE* 3.4 36.1 - - + -
341B MET 2.8 21.1 + - - +
342B PHE 3.5 4.3 - - - +
344B ALA* 1.3 78.5 - - - +
346B GLN* 1.3 62.7 + - - +
348B VAL* 4.3 0.5 - - - +
349B ALA* 3.2 26.2 + - - +
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Residues in contact with GLN 346 (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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29B CYS* 4.1 9.6 - - - -
73B LEU* 2.6 46.8 + - + +
76B ASN* 2.6 37.8 + - - +
77B PHE 4.0 5.5 - - - +
342B PHE* 3.1 44.7 + - + +
343B PHE* 3.2 7.4 + - + +
345B ALA* 1.3 76.0 - - - +
347B PHE* 1.3 57.0 + - - +
349B ALA* 4.4 0.9 - - - -
350B TRP* 2.9 53.6 + - + +
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Residues in contact with PHE 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B PHE* 4.4 9.6 - + + -
28B PHE* 3.3 35.0 - + + -
29B CYS* 3.8 10.0 - - - -
32B LEU* 3.9 25.9 - - + +
343B PHE 2.9 16.4 + - - +
344B ALA* 3.6 6.7 - - - +
345B ALA 3.2 0.2 - - - -
346B GLN* 1.3 75.6 - - - +
348B VAL* 1.3 72.2 + - + +
350B TRP* 3.3 2.5 + - - -
351B PHE* 2.7 61.5 + + - +
401B SER 4.6 4.5 - - - -
402B ILE* 3.8 28.5 - - + -
405B PRO* 4.0 16.6 - - + -
406B VAL* 5.3 1.1 - - + -
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Residues in contact with VAL 348 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 4.0 20.9 - - + -
186B LEU* 5.6 2.7 - - + -
189B GLU* 3.9 36.3 - - + +
190B ALA 4.6 0.4 - - - +
193B ILE* 4.6 6.5 - - + +
344B ALA* 3.1 18.3 + - + +
345B ALA 4.4 2.0 - - - +
347B PHE* 1.3 84.9 - - + +
349B ALA* 1.3 57.9 + - - +
351B PHE* 3.4 5.5 - - - +
352B ASN* 2.8 30.4 + - + +
401B SER 4.6 6.1 - - - +
405B PRO* 4.2 25.1 - - + -
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Residues in contact with ALA 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B TYR* 2.9 23.2 + - - +
76B ASN* 3.6 28.3 - - + +
345B ALA 3.2 20.0 + - - +
346B GLN 4.1 1.3 - - - +
348B VAL* 1.3 75.1 - - - +
350B TRP* 1.3 60.4 + - - +
352B ASN* 3.6 5.3 + - - +
353B TYR* 2.9 22.5 + - - +
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Residues in contact with TRP 350 (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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29B CYS* 3.3 46.0 - - + -
30B LEU* 5.9 2.0 - - + -
32B LEU* 4.1 12.5 - - + +
33B LEU* 3.8 29.8 - - + -
60B LEU* 3.8 17.8 - - + +
68B TYR* 3.8 20.8 - + - -
69B LEU* 3.5 30.1 + - + +
73B LEU* 4.4 16.0 - - + +
76B ASN* 4.0 8.2 - - - +
346B GLN* 2.9 49.3 + - + +
349B ALA* 1.3 74.3 - - - +
351B PHE* 1.3 55.2 + - - +
353B TYR* 4.4 4.0 - - - +
354B SER* 2.7 36.7 + - - -
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Residues in contact with PHE 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.0 19.5 - - + +
193B ILE* 3.8 12.1 - - + -
347B PHE* 2.7 45.8 + + + +
348B VAL* 3.4 7.2 - - - +
350B TRP* 1.3 77.4 - - - +
352B ASN* 1.3 62.8 + - - +
354B SER* 3.3 11.2 + - - -
356B LEU* 3.5 17.5 + - + -
357B GLY* 3.1 56.5 + - - -
360B LEU* 4.0 22.9 - - + -
405B PRO* 3.5 27.8 - - + -
406B VAL* 4.6 5.4 - - + -
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Residues in contact with ASN 352 (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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189B GLU 5.1 0.8 + - - -
192B HIS* 3.6 30.3 + - - +
193B ILE* 3.8 28.1 - - + +
348B VAL* 2.8 19.3 + - + +
349B ALA* 3.8 5.4 - - - +
351B PHE* 1.3 73.8 - - - +
353B TYR* 1.3 68.9 + - - +
355B GLN* 2.9 27.8 + - - +
357B GLY* 5.2 1.1 - - - +
358B LEU* 5.8 0.8 - - - +
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Residues in contact with TYR 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B HIS* 4.2 24.5 + - + +
59B SER 4.5 7.4 + - - -
60B LEU* 3.6 21.8 - - + -
62B ASP* 5.2 0.2 + - - -
64B ASP* 3.5 31.2 + - - +
65B GLY* 3.7 7.6 + - - -
68B TYR* 3.4 52.7 - + + -
349B ALA 2.9 23.0 + - - +
350B TRP 4.3 1.1 - - - +
351B PHE 3.5 0.2 - - - -
352B ASN* 1.3 77.7 + - - +
354B SER* 1.3 62.1 + - - +
355B GLN* 3.0 19.0 + - - +
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Residues in contact with SER 354 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 4.8 0.7 - - - +
36B THR* 3.5 26.9 - - - +
57B ALA* 3.5 3.8 - - - -
58B HIS* 3.0 35.1 + - - +
60B LEU* 4.4 7.4 - - - -
350B TRP 2.7 22.8 + - - -
351B PHE* 3.3 8.5 + - - -
353B TYR* 1.3 79.3 - - - +
355B GLN* 1.3 63.9 + - - +
356B LEU* 3.1 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
------------------------------------------------------------
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