Contacts of the helix formed by residues 80 - 97 (chain F) in PDB entry 4DHX
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 PRO 80 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F LEU* 4.3 4.7 - - + -
40F CYS* 3.9 29.6 - - + -
42F TRP* 4.7 0.7 - - + -
78F LEU 3.2 9.8 - - - +
79F VAL* 1.3 94.0 - - + +
81F ASP* 1.3 64.2 + - - +
82F SER* 3.7 18.2 - - - +
83F VAL* 3.2 24.8 + - + +
84F LYS* 3.4 7.8 + - - +
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Residues in contact with ASP 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F VAL 3.5 2.6 + - - -
80F PRO* 1.3 69.4 - - - +
82F SER* 1.3 82.6 + - - +
84F LYS* 3.3 19.2 + - + +
85F LYS* 2.9 32.9 + - - +
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Residues in contact with SER 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F PRO* 3.7 13.9 - - - +
81F ASP* 1.3 86.8 + - - +
83F VAL* 1.3 65.7 + - - +
85F LYS* 3.1 33.2 - - - +
86F GLU* 3.1 33.1 + - - +
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Residues in contact with VAL 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU* 3.7 30.1 - - + -
36F LYS* 4.0 38.1 - - + +
37F LEU* 4.5 7.4 - - + -
40F CYS* 4.9 3.8 - - + -
79F VAL* 4.8 3.1 - - + -
80F PRO* 3.2 33.8 + - + +
82F SER* 1.3 87.4 + - - +
84F LYS* 1.3 61.6 + - + +
86F GLU* 3.5 9.7 + - - +
87F LEU* 3.1 22.8 + - + +
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Residues in contact with LYS 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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1212D CYS* 3.7 8.9 - - - -
1216D VAL* 4.7 23.3 - - + -
33F LEU* 6.4 0.2 - - - -
76F ARG 4.6 7.2 + - - -
79F VAL* 3.6 39.6 + - + +
80F PRO 3.4 6.5 + - - +
81F ASP* 3.3 20.4 + - + +
83F VAL* 1.3 76.4 - - + +
85F LYS* 1.3 59.6 + - - +
87F LEU* 3.1 8.0 + - - +
88F LEU* 2.9 28.5 + - - +
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Residues in contact with LYS 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81F ASP* 2.9 16.6 + - - +
82F SER* 3.1 40.3 - - - +
84F LYS* 1.3 76.9 - - - +
86F GLU* 1.3 65.7 + - + +
88F LEU* 3.4 13.3 + - + +
89F GLN* 3.0 27.4 + - - +
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Residues in contact with GLU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LYS* 2.6 41.2 + - - +
82F SER* 3.1 31.1 + - - +
83F VAL* 3.7 7.3 - - - +
84F LYS 3.2 0.2 - - - -
85F LYS* 1.3 90.3 - - + +
87F LEU* 1.3 62.4 + - - +
89F GLN* 3.4 7.2 + - - +
90F ARG* 3.2 29.0 + - + +
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Residues in contact with LEU 87 (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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1212D CYS* 4.0 10.3 - - - +
1215D LEU* 5.9 2.5 - - + -
1216D VAL* 3.8 26.5 - - + +
1219D PHE* 5.4 3.4 - - + -
29F LEU* 4.5 28.7 - - + +
32F LEU* 4.7 18.2 - - + -
33F LEU* 4.0 37.0 - - + +
36F LYS* 4.9 7.6 - - + -
83F VAL 3.1 15.0 + - - +
84F LYS* 3.5 9.0 - - - +
86F GLU* 1.3 75.6 - - - +
88F LEU* 1.3 63.7 + - - +
90F ARG* 3.2 8.7 + - - +
91F ILE* 3.1 30.2 + - + +
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Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1208D CYS* 3.6 35.0 - - + +
1209D GLU* 3.7 31.2 - - + +
1212D CYS* 3.6 14.7 - - + -
84F LYS 2.9 16.1 + - - +
85F LYS* 3.6 13.0 - - + +
86F GLU 3.3 0.2 - - - -
87F LEU* 1.3 75.8 - - - +
89F GLN* 1.3 58.2 + - - +
91F ILE* 3.4 3.0 + - + +
92F ARG* 3.0 44.8 + - - +
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Residues in contact with GLN 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85F LYS 3.0 16.9 + - - +
86F GLU* 3.6 8.5 - - - +
87F LEU 3.1 0.6 - - - -
88F LEU* 1.3 76.6 - - - +
90F ARG* 1.3 62.0 + - + +
92F ARG* 3.3 20.7 + - - +
93F THR* 2.9 45.4 + - - +
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Residues in contact with ARG 90 (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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25F GLU* 4.9 8.8 + - - +
29F LEU* 4.2 20.7 - - + +
32F LEU* 3.3 35.6 - - - +
36F LYS* 6.0 1.8 - - - +
86F GLU* 3.2 16.2 + - - +
87F LEU* 3.2 11.4 + - - +
89F GLN* 1.3 76.5 - - + +
91F ILE* 1.3 57.2 + - - +
93F THR* 3.5 6.5 + - - -
94F PHE* 2.9 31.6 + - - +
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Residues in contact with ILE 91 (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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1208D CYS* 4.5 15.9 - - + +
1211D VAL* 4.7 2.7 - - + -
1212D CYS* 3.6 39.5 - - + +
1215D LEU* 4.1 11.2 - - + -
16F ILE* 5.0 1.6 - - + -
20F LEU* 4.6 14.4 - - + -
25F GLU* 6.0 0.4 - - - -
29F LEU* 3.7 30.1 - - + -
87F LEU* 3.1 16.7 + - + +
88F LEU* 3.7 7.4 - - - +
89F GLN 3.2 0.2 - - - -
90F ARG* 1.3 74.1 - - - +
92F ARG* 1.3 65.6 + - - +
94F PHE* 3.4 5.6 + - - +
95F LEU* 3.0 48.9 + - + +
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Residues in contact with ARG 92 (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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1204D VAL* 4.8 4.0 + - - +
1205D ALA* 3.3 39.0 - - - +
1208D CYS* 3.9 26.0 - - + +
1209D GLU* 6.1 0.2 - - - -
88F LEU* 3.0 38.3 + - - +
89F GLN* 3.3 22.6 + - - +
91F ILE* 1.3 76.9 - - - +
93F THR* 1.3 61.4 + - - +
95F LEU* 4.0 1.8 - - - +
96F ALA* 3.1 27.0 + - - +
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Residues in contact with THR 93 (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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89F GLN* 2.9 36.5 + - - +
90F ARG* 3.7 7.2 - - - -
92F ARG* 1.3 73.6 - - - +
94F PHE* 1.3 67.2 + - - +
96F ALA* 3.3 6.2 + - - +
97F GLN* 3.0 36.3 + - + +
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Residues in contact with PHE 94 (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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19F LYS* 4.5 11.7 - - + -
20F LEU* 3.6 23.8 - - + -
23F THR* 3.2 33.4 - - + -
25F GLU* 3.6 36.1 - - + +
28F ARG* 4.4 5.6 - - - -
90F ARG 2.9 19.0 + - - +
91F ILE* 3.4 3.3 + - - +
93F THR* 1.3 79.0 - - - +
95F LEU* 1.3 80.7 + - + +
97F GLN* 3.4 4.5 + - - -
98F HIS* 2.6 66.9 + + - -
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Residues in contact with LEU 95 (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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1204D VAL* 6.0 2.2 - - + -
1208D CYS* 3.4 32.5 - - - -
16F ILE* 3.5 43.3 - - + +
19F LYS* 5.0 8.7 - - + -
20F LEU* 4.5 5.8 - - + -
91F ILE* 3.0 25.1 + - + +
92F ARG* 4.0 3.4 - - - +
94F PHE* 1.3 94.6 - - + +
96F ALA* 1.3 57.6 + - - +
97F GLN 3.0 4.7 - - - -
98F HIS* 2.9 31.3 + - + +
99F ALA 3.9 2.9 - - - +
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Residues in contact with ALA 96 (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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92F ARG 3.1 18.8 + - - +
93F THR* 3.9 5.2 - - - +
95F LEU* 1.3 75.6 - - - +
97F GLN* 1.3 57.7 + - - +
98F HIS 3.3 1.1 + - - -
99F ALA 4.4 8.5 + - - +
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Residues in contact with GLN 97 (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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93F THR* 3.0 30.1 + - + +
94F PHE* 3.8 6.8 - - - +
95F LEU 3.0 1.2 - - - -
96F ALA* 1.3 78.2 - - - +
98F HIS* 1.3 74.0 + - + +
99F ALA 4.1 1.3 + - - -
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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