Contacts of the helix formed by residues 72 - 86 (chain F) in PDB entry 4DEM
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 72 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F LYS* 4.6 10.8 - - + -
31F PHE* 3.8 21.8 - + + -
32F VAL* 3.6 29.7 - - + +
67F ALA 3.6 20.0 - - - -
68F ILE* 3.2 18.2 - - + +
69F GLY* 2.8 24.6 + - - -
70F GLY* 3.3 20.7 - - - -
71F LYS* 1.3 88.2 - - - +
73F ASN* 1.3 65.8 + - - +
74F ARG 3.3 2.9 + - - -
75F GLY 3.4 0.5 + - - -
76F LEU* 2.9 27.2 + - + +
104F TRP* 3.8 20.2 - + - -
107F GLU* 3.4 26.3 + - - -
127F ARG* 6.0 0.2 - - - -
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Residues in contact with ASN 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F TYR* 4.0 7.8 - - + -
71F LYS* 3.1 27.5 - - + +
72F TYR* 1.3 80.4 - - - +
74F ARG* 1.3 67.7 + - + +
76F LEU* 3.9 5.6 - - - +
77F THR* 2.8 30.4 + - - +
107F GLU* 4.1 0.2 + - - -
253F PHE* 5.7 7.2 - - + -
358F LEU* 6.1 3.8 - - + -
361F LYS* 3.3 39.5 + - + +
362F ILE* 5.5 7.4 - - + +
367F LYS 6.0 0.4 + - - -
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Residues in contact with ARG 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F TYR 3.3 0.4 - - - -
73F ASN* 1.3 81.2 - - + +
75F GLY* 1.3 63.2 + - - +
77F THR* 3.1 21.4 + - - -
78F VAL* 3.5 1.6 + - - +
106F VAL* 3.7 22.4 - - + -
107F GLU* 3.5 8.1 + - - +
110F GLN* 3.5 37.0 + - - +
127F ARG* 5.7 0.6 - - - +
215F THR* 5.4 0.6 - - - +
218F TYR* 3.5 29.3 + - - -
219F SER* 2.8 50.6 + - - +
223F PRO* 3.5 14.5 - - + +
253F PHE* 3.8 28.0 - - - -
401F YS4 6.1 0.2 + - - -
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Residues in contact with GLY 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F PHE* 4.0 10.5 - - - -
74F ARG* 1.3 77.7 - - - +
76F LEU* 1.3 59.9 + - - +
78F VAL* 3.1 18.9 + - - +
79F VAL* 3.5 6.9 + - - +
103F GLY* 3.2 34.0 - - - -
106F VAL* 4.5 2.0 - - - +
107F GLU* 2.8 17.5 + - - +
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Residues in contact with LEU 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24F TYR* 3.7 39.7 - - + +
27F GLU* 3.8 29.8 - - + +
28F LYS* 3.9 16.6 - - + -
31F PHE* 3.6 36.9 - - + -
71F LYS 4.1 14.1 - - - +
72F TYR* 2.9 24.3 + - + +
73F ASN* 4.0 2.2 - - - +
75F GLY* 1.3 75.1 - - - +
77F THR* 1.3 63.6 + - - +
79F VAL* 3.2 7.3 + - + +
80F VAL* 2.9 27.3 + - + +
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Residues in contact with THR 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F TYR* 2.9 28.3 + - - +
73F ASN 2.8 19.0 + - - -
74F ARG* 3.3 12.6 - - - -
75F GLY 3.1 0.6 - - - -
76F LEU* 1.3 78.3 - - - +
78F VAL* 1.3 63.3 + - - +
80F VAL* 4.1 0.8 - - - +
81F ALA* 3.0 23.4 + - - +
219F SER 5.7 0.4 + - - -
223F PRO* 3.9 16.8 - - + -
224F ILE* 3.4 31.6 - - + -
358F LEU* 3.7 18.6 - - + +
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Residues in contact with VAL 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F ARG 4.0 1.3 - - - +
75F GLY 3.1 9.0 + - - +
77F THR* 1.3 79.5 - - - +
79F VAL* 1.3 57.5 + - - +
82F PHE* 2.8 29.0 + - + +
99F ALA* 3.7 21.5 - - + +
102F VAL* 4.1 13.5 - - + +
103F GLY* 3.8 14.1 - - - +
106F VAL* 3.7 21.1 - - + -
223F PRO* 3.6 40.2 - - + +
226F ALA* 4.6 4.0 - - + -
227F ALA* 3.7 10.6 - - + +
230F MET* 4.7 7.4 - - - -
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Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27F GLU* 3.9 26.7 - - + +
31F PHE* 3.8 15.7 - - + -
75F GLY 3.5 11.6 + - - +
76F LEU* 3.2 10.4 + - + +
78F VAL* 1.3 79.2 - - - +
80F VAL* 1.3 63.3 + - - +
82F PHE* 3.2 6.9 + - + +
83F ARG* 3.0 27.1 + - + +
96F LEU* 6.2 2.7 - - + -
99F ALA* 3.9 21.5 - - + +
100F TRP* 3.5 37.7 - - + +
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Residues in contact with VAL 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23F VAL* 3.6 30.7 - - + +
24F TYR* 4.1 30.7 - - + +
27F GLU* 3.8 26.7 - - + -
76F LEU* 2.9 22.8 + - + +
77F THR 4.1 2.2 - - - +
79F VAL* 1.3 71.7 - - - +
81F ALA* 1.3 63.7 + - - +
83F ARG* 3.2 7.4 + - - +
84F GLU* 3.1 51.5 + - - +
353F ALA 5.8 0.9 - - - +
354F VAL 5.8 2.5 - - - +
357F GLY* 6.1 0.7 - - - -
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F THR 3.0 19.8 + - - +
80F VAL* 1.3 77.4 - - - +
82F PHE* 1.3 56.9 + - - +
84F GLU* 3.1 9.5 + - - -
85F LEU* 2.8 41.8 + - + +
224F ILE* 3.7 24.0 - - + -
227F ALA* 3.6 20.4 - - + -
354F VAL* 4.4 6.5 - - + -
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Residues in contact with PHE 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F VAL* 2.8 21.3 + - + +
79F VAL* 3.2 5.8 + - + +
81F ALA* 1.3 75.0 - - - +
83F ARG* 1.3 62.0 + - + +
85F LEU* 4.5 1.3 - - - +
86F VAL* 2.9 68.6 + - + +
91F GLN* 4.3 9.2 - - + -
95F SER* 3.7 39.9 - - - -
96F LEU* 4.0 24.5 - - + -
99F ALA* 3.7 20.9 - - + -
166F TYR* 5.9 0.7 - + - -
227F ALA* 3.8 10.5 - - + +
230F MET* 4.0 38.6 - - + -
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Residues in contact with ARG 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F VAL* 6.5 0.7 - - + -
27F GLU* 3.1 37.6 + - - +
30F ASP* 5.0 6.5 + - - -
79F VAL* 3.0 17.9 + - + +
80F VAL 3.5 8.7 - - - +
82F PHE* 1.3 79.3 - - + +
84F GLU* 1.3 61.3 + - + +
86F VAL 3.7 2.6 - - - +
88F PRO* 5.6 1.6 - - - +
91F GLN* 2.8 54.0 + - - +
96F LEU* 3.5 35.6 - - + +
100F TRP* 4.8 14.1 - - - +
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Residues in contact with GLU 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F VAL* 4.0 15.6 - - + +
80F VAL* 3.1 40.8 + - + +
81F ALA* 3.1 1.6 + - - +
83F ARG* 1.3 79.6 - - + +
85F LEU* 1.3 60.9 + - - +
86F VAL 3.6 1.2 - - - +
351F PRO* 3.8 20.8 - - + +
353F ALA* 3.8 16.0 - - + +
354F VAL* 3.2 46.9 - - + +
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Residues in contact with LEU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F ALA* 2.8 26.1 + - + +
82F PHE* 4.2 2.0 - - - +
84F GLU* 1.3 80.1 - - - +
86F VAL* 1.3 60.9 + - - +
87F GLU 3.9 1.2 + - - -
224F ILE* 4.9 0.9 - - + +
227F ALA* 4.2 5.8 - - + -
228F MET* 3.9 40.8 - - + +
231F ALA* 3.9 19.2 - - + +
233F ILE* 4.0 9.7 - - + +
350F LEU* 4.0 22.9 - - + -
351F PRO* 3.8 27.4 - - + -
354F VAL* 4.2 13.5 - - + -
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Residues in contact with VAL 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82F PHE* 2.9 50.5 + - + +
83F ARG 3.7 2.9 - - - +
84F GLU 4.8 0.7 - - - +
85F LEU* 1.3 81.1 + - - +
87F GLU* 1.3 71.0 + - - +
88F PRO* 3.3 3.6 - - - +
90F LYS* 3.8 23.1 - - + +
91F GLN* 2.8 39.0 + - + -
230F MET 4.8 0.4 - - - +
231F ALA* 3.6 26.0 - - + -
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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