Contacts of the helix formed by residues 84 - 98 (chain B) in PDB entry 4C1M
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 LEU 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B SER* 1.3 71.5 - - - +
85B MET* 1.3 57.2 + - - +
87B MET* 2.9 43.1 + - + +
88B GLN* 3.0 12.3 + - - +
245D GLU* 5.6 4.3 - - + +
338D LEU 4.0 13.9 - - - +
340D GLN* 3.7 28.3 - - + +
342D PHE 4.8 2.9 - - - +
344D PHE* 3.8 34.8 - - + +
383D GLY 4.8 2.9 - - - +
384D LEU* 3.3 27.6 + - + +
387D THR* 2.9 24.3 + - - +
388D PRO 4.1 2.2 - - - +
389D ALA* 3.7 4.4 - - - +
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Residues in contact with MET 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B SER* 3.3 13.0 - - - +
84B LEU* 1.3 76.3 - - - +
86B PHE* 1.3 55.2 - - - +
88B GLN* 4.2 5.2 - - - +
89B TRP* 2.9 30.0 + - - +
249D MET* 3.7 39.5 - - - +
381D LEU* 4.3 5.6 - - + +
384D LEU* 3.1 40.3 + - + +
385D MET* 4.2 11.0 - - + +
533D LEU* 3.8 8.3 - - + -
537D ILE* 4.0 24.0 - - + -
551D ILE* 4.1 12.6 - - + +
552D PHE* 3.6 18.6 - - + -
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Residues in contact with PHE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ARG* 3.8 31.2 - - + -
83B SER* 2.9 16.7 + - - +
85B MET* 1.3 75.9 - - - +
87B MET* 1.3 64.8 + - - +
90B GLY* 3.6 2.1 + - - -
296D TYR* 3.4 32.3 - + - -
299D LEU* 3.9 22.0 - - + -
300D VAL* 3.7 34.3 - - + -
334D TYR* 3.8 5.6 - - - -
338D LEU* 3.8 28.8 - - + +
389D ALA* 4.9 2.2 - - + -
490D ARG* 4.1 15.5 - - + -
552D PHE* 3.7 38.7 - - + +
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Residues in contact with MET 87 (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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83B SER 3.8 1.2 + - - +
84B LEU* 2.9 40.0 + - + +
86B PHE* 1.3 82.5 - - - +
88B GLN* 1.3 88.3 + - + +
90B GLY* 3.2 10.6 + - - -
91B GLN* 3.3 1.1 + - - +
605B HEM 3.2 48.3 - - + +
243D MET* 4.3 16.8 - - + -
245D GLU* 5.4 1.3 - - - +
338D LEU* 3.9 42.8 - - + +
339D ILE* 4.1 20.6 - - + -
340D GLN 5.4 0.4 - - - +
384D LEU* 5.0 2.5 - - + -
389D ALA* 5.2 1.1 - - + +
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Residues in contact with GLN 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU 3.0 14.4 + - - +
85B MET* 3.3 7.4 + - - +
87B MET* 1.3 81.5 - - - +
89B TRP* 1.3 59.4 + - - +
91B GLN* 2.8 22.5 + - - +
92B LEU* 3.0 26.3 + - - +
243D MET* 3.3 17.7 - - - +
245D GLU* 3.2 35.9 - - + +
246D LEU* 3.3 33.4 - - - +
249D MET* 3.8 14.4 - - + -
384D LEU* 4.1 14.6 - - + -
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Residues in contact with TRP 89 (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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85B MET* 2.9 18.3 + - + +
86B PHE 4.5 0.2 - - - +
88B GLN* 1.3 73.9 - - - +
90B GLY* 1.3 55.7 + - - +
92B LEU* 3.7 19.4 - - + +
93B LEU* 2.7 44.4 + - + +
249D MET* 3.8 16.4 - - + -
253D LEU* 5.0 7.2 - - + -
288D VAL* 3.9 28.7 - - + -
291D ILE* 3.6 33.9 - - + -
292D THR* 3.1 30.3 + - - +
296D TYR* 3.7 33.0 - + + -
533D LEU* 3.8 38.1 - - + -
552D PHE* 3.5 16.2 - + + -
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Residues in contact with GLY 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE 3.6 5.2 + - - -
87B MET 3.2 8.4 + - - -
89B TRP* 1.3 79.4 - - - +
91B GLN* 1.3 56.3 + - - +
93B LEU* 3.7 2.2 - - - +
94B ASP* 2.8 29.8 + - - +
605B HEM 3.7 12.6 - - - -
296D TYR* 3.4 29.9 - - - -
332D PHE* 3.5 6.0 - - - -
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Residues in contact with GLN 91 (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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87B MET* 3.3 7.0 + - - +
88B GLN* 2.8 29.1 + - - +
89B TRP 3.3 0.2 - - - -
90B GLY* 1.3 74.4 - - - +
92B LEU* 1.3 64.2 + - - +
94B ASP* 3.1 4.0 + - - +
95B HIS* 3.0 36.1 + - + -
605B HEM 3.8 36.4 - - + +
606B NIH 3.1 31.4 + - - +
242D GLU* 2.9 26.5 + - - -
243D MET* 3.4 17.5 - - - +
246D LEU* 3.6 13.9 - - + +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLN 3.0 18.4 + - - +
89B TRP* 3.7 30.3 - - + +
91B GLN* 1.3 76.3 - - - +
93B LEU* 1.3 62.4 + - - +
95B HIS* 3.1 18.1 + - + +
96B ASP* 3.4 8.1 + - - +
175D MET* 3.7 31.3 - - + +
246D LEU* 4.0 22.6 - - + +
249D MET* 3.8 25.4 - - + -
250D HIS* 4.1 15.9 - - + +
253D LEU* 3.8 23.6 - - + -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TRP* 2.7 28.0 + - + +
90B GLY 3.7 1.6 - - - +
92B LEU* 1.3 70.0 - - - +
94B ASP* 1.3 65.6 + - - +
95B HIS 3.1 1.8 - - - -
96B ASP* 2.9 18.4 + - + +
97B LEU* 3.1 32.9 - - + +
171D VAL* 4.2 19.1 - - + -
175D MET* 5.5 1.6 - - - -
288D VAL* 4.8 5.6 - - + -
292D THR* 3.4 41.7 - - + +
296D TYR* 3.9 23.8 - - + -
332D PHE* 4.1 4.0 - - + -
503D PHE* 3.7 20.4 - - + -
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLY 2.8 18.1 + - - +
91B GLN 3.3 10.8 - - - +
93B LEU* 1.3 71.7 - - - +
95B HIS* 1.3 67.3 - - + +
97B LEU* 3.0 8.0 + - - +
98B ASP* 2.9 33.9 + - - +
605B HEM 1.8 74.2 - - + +
332D PHE* 3.5 17.7 - - + -
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Residues in contact with HIS 95 (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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91B GLN* 3.0 16.5 + - + -
92B LEU* 3.3 12.8 - - - +
93B LEU 3.1 0.4 - - - -
94B ASP* 1.3 80.0 - - - +
96B ASP* 1.3 54.9 + - - +
97B LEU 3.3 0.2 - - - -
606B NIH 2.6 42.6 + - - -
167D LEU* 3.2 19.3 - - - +
174D SER* 4.9 0.3 + - - -
175D MET* 3.5 20.5 + - + +
237D ASP* 3.6 22.7 + - + +
239D ARG* 3.3 35.2 + - + +
246D LEU* 3.4 36.3 - - + +
250D HIS* 4.6 4.8 + - - +
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Residues in contact with ASP 96 (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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92B LEU 3.4 3.9 + - - +
93B LEU* 2.9 17.1 + - + +
95B HIS* 1.3 77.2 - - - +
97B LEU* 1.3 53.9 + - + +
167D LEU* 4.4 2.2 - - - +
168D THR 2.7 10.9 - - - +
170D PHE 3.0 6.6 - - - +
171D VAL* 3.7 8.1 - - - +
172D ASP* 3.0 15.1 + - - +
173D ALA* 3.0 23.7 + - - -
174D SER* 3.0 13.1 + - - -
175D MET* 3.8 14.9 - - + +
288D VAL* 3.7 15.4 - - - +
1579D CA 2.2 59.1 - - - -
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Residues in contact with LEU 97 (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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93B LEU* 3.1 25.1 - - + +
94B ASP* 3.0 7.7 + - - +
96B ASP* 1.3 85.9 - - + +
98B ASP* 1.3 67.7 + - - +
165D ASN* 2.9 20.8 + - - +
167D LEU* 4.3 2.2 - - - -
168D THR 3.8 3.1 - - - +
169D SER* 3.2 26.1 - - - +
170D PHE 4.3 1.6 - - - +
171D VAL* 3.9 18.6 - - + -
324D ILE* 3.3 14.5 - - + +
328D PHE* 3.8 19.7 - - + -
332D PHE* 4.9 0.4 - - + -
503D PHE* 3.7 29.8 - - + -
506D LEU* 3.7 15.5 - - + -
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Residues in contact with ASP 98 (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 PHE* 4.2 11.4 - - + -
94B ASP* 2.9 21.0 + - - +
97B LEU* 1.3 87.1 - - - +
99B PHE* 1.3 55.9 + - - +
605B HEM 2.8 39.1 - - - +
165D ASN* 3.3 17.0 - - - +
167D LEU* 3.4 7.0 - - - +
239D ARG* 2.9 27.0 + - - -
324D ILE* 4.3 4.0 - - + +
328D PHE* 3.7 17.8 - - - -
329D THR* 3.6 15.4 - - - +
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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