Contacts of the helix formed by residues 79 - 96 (chain F) in PDB entry 3SRF
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 THR 79 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F GLY* 1.3 78.2 - - - -
80F HIS* 1.3 65.7 + - - +
81F GLU* 3.5 13.6 + - - +
82F TYR* 3.4 26.7 + - - +
83F HIS* 3.2 17.1 + - - -
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Residues in contact with HIS 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75F PHE* 4.3 5.4 - + - -
79F THR* 1.3 75.4 - - - +
81F GLU* 1.3 65.0 + - - +
83F HIS* 3.7 2.4 + - - +
84F ALA* 3.2 24.4 + - - +
223F LYS* 5.2 3.1 + - - -
226F GLN* 3.3 31.2 + - + +
227F ASP* 2.9 32.1 + - - -
230F PHE* 3.1 48.0 - + + -
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Residues in contact with GLU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F THR* 3.3 11.6 + - - +
80F HIS* 1.3 79.0 - - - +
82F TYR* 1.3 62.2 + - - +
84F ALA* 3.3 8.0 + - - +
85F GLU* 3.1 29.7 + - - +
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Residues in contact with TYR 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ILE 5.6 5.2 - - - -
51F GLY* 4.4 1.4 - - - -
52F PRO* 3.9 24.6 - - - +
55F ARG* 3.3 56.4 + - - +
77F HIS 6.1 0.4 - - - -
78F GLY* 4.5 10.1 - - - -
79F THR* 3.4 23.1 + - - +
80F HIS 3.3 0.4 - - - -
81F GLU* 1.3 81.0 - - - +
83F HIS* 1.3 75.8 + + - +
85F GLU* 3.2 7.9 + - - +
86F THR* 2.9 33.3 + - - -
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Residues in contact with HIS 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73F LEU* 4.1 15.9 - - + +
74F ASN 3.3 24.9 + - - -
75F PHE* 3.5 50.5 - + + -
77F HIS 2.7 29.7 + - - -
78F GLY 4.0 3.2 + - - -
79F THR 3.2 22.2 + - - +
80F HIS* 4.3 3.6 - - - +
81F GLU 3.4 0.4 - - - -
82F TYR* 1.3 88.9 - + - +
84F ALA* 1.3 59.8 - - - +
86F THR* 3.2 8.3 + - - +
87F ILE* 2.8 35.5 + - - +
230F PHE* 4.4 2.7 - - + -
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Residues in contact with ALA 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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80F HIS 3.2 20.0 + - - +
81F GLU* 3.5 8.5 - - - +
83F HIS* 1.3 75.4 - - - +
85F GLU* 1.3 56.9 + - - +
87F ILE* 3.8 8.0 - - - +
88F LYS* 3.1 25.6 + - - +
230F PHE* 3.7 18.5 - - + -
234F GLN* 4.0 14.2 - - - +
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Residues in contact with GLU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F ARG* 3.0 26.7 + - - +
81F GLU* 3.1 21.3 + - + +
82F TYR* 3.4 10.9 - - - +
83F HIS 3.1 0.2 - - - -
84F ALA* 1.3 75.7 - - - +
86F THR* 1.3 65.1 + - - +
87F ILE 3.3 0.2 - - - -
88F LYS* 3.3 9.9 + - + +
89F ASN* 3.0 41.7 + - - +
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Residues in contact with THR 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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50F ILE* 3.8 41.1 - - + +
55F ARG* 3.4 24.6 + - + +
73F LEU* 4.2 18.4 - - + -
82F TYR* 2.9 22.8 + - - -
83F HIS* 3.4 13.7 + - - +
85F GLU* 1.3 75.2 - - - +
87F ILE* 1.3 60.7 + - - +
89F ASN* 3.3 7.1 + - - +
90F VAL* 3.0 30.9 + - + +
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Residues in contact with ILE 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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73F LEU* 3.6 25.4 - - + -
75F PHE* 6.0 0.7 - - + -
83F HIS 2.8 20.7 + - - +
84F ALA* 3.8 5.4 - - - +
86F THR* 1.3 76.7 - - - +
88F LYS* 1.3 63.5 + - - +
90F VAL* 3.2 7.4 + - - +
91F ARG* 3.0 61.1 + - + +
109F VAL* 4.2 13.2 - - + -
111F LEU* 6.4 0.7 - - + -
230F PHE* 4.6 5.6 - - + -
234F GLN* 3.7 39.7 - - + +
236F VAL* 4.7 10.3 - - + -
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Residues in contact with LYS 88 (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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84F ALA 3.1 19.0 + - - +
85F GLU* 3.3 12.7 + - + +
87F ILE* 1.3 77.0 - - - +
89F ASN* 1.3 62.8 + - - +
91F ARG* 3.4 5.3 + - - +
92F THR* 2.6 41.6 + - - +
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Residues in contact with ASN 89 (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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55F ARG* 2.8 41.8 + - - +
56F SER* 4.4 4.2 - - - +
57F VAL* 3.6 24.0 - - + +
60F LEU* 3.6 8.4 - - + +
85F GLU* 3.0 32.4 + - - +
86F THR 3.5 5.4 - - - +
88F LYS* 1.3 82.4 - - - +
90F VAL* 1.3 59.9 + - - +
92F THR* 3.8 3.0 - - - -
93F ALA* 3.1 24.4 + - - +
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Residues in contact with VAL 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F ILE* 4.6 5.8 - - + -
60F LEU* 3.8 27.6 - - + -
64F ILE* 4.8 1.2 - - + +
68F MET* 5.2 4.0 - - + -
71F ALA* 4.2 22.4 - - + -
73F LEU* 5.5 2.2 - - + -
86F THR* 3.0 27.5 + - + +
87F ILE* 3.2 7.8 + - - +
89F ASN* 1.3 75.5 - - - +
91F ARG* 1.3 55.5 + - + +
93F ALA* 3.4 4.5 + - - +
94F THR* 2.7 42.8 + - - +
107F VAL* 4.5 11.0 - - + +
109F VAL* 4.2 22.4 - - + -
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Residues in contact with ARG 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F ILE* 3.0 40.7 + - + +
88F LYS* 4.0 4.9 - - - +
90F VAL* 1.3 74.6 - - + +
92F THR* 1.3 57.3 + - - +
94F THR* 3.5 6.8 - - - -
95F GLU* 2.8 41.7 + - + +
109F VAL* 4.8 20.3 - - + +
234F GLN* 2.7 33.7 + - - -
235F ASP* 3.2 22.3 + - - +
236F VAL* 4.8 2.0 - - - +
237F ASP* 5.8 0.4 + - - -
460F ARG* 6.0 4.8 - - - +
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Residues in contact with THR 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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57F VAL* 4.4 17.9 - - + -
61F LYS* 5.0 1.1 - - - -
88F LYS* 2.6 34.6 + - - +
89F ASN* 3.8 7.0 - - - -
91F ARG* 1.3 74.1 - - - +
93F ALA* 1.3 58.9 + - - +
95F GLU* 3.3 5.9 + - + +
96F SER* 3.0 28.9 + - - -
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Residues in contact with ALA 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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57F VAL* 4.0 7.1 - - + +
60F LEU* 3.7 26.5 - - + -
61F LYS* 3.8 25.5 - - + +
64F ILE* 3.6 5.8 - - + +
89F ASN 3.1 15.8 + - - +
90F VAL* 3.7 4.7 - - - +
92F THR* 1.3 79.4 - - - +
94F THR* 1.3 56.7 + - - +
96F SER* 2.9 19.7 + - - -
97F PHE* 3.2 16.6 - - - -
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Residues in contact with THR 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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64F ILE* 3.9 14.3 - - - +
90F VAL* 2.7 26.6 + - - +
91F ARG* 3.5 8.2 - - - -
93F ALA* 1.3 75.2 - - - +
95F GLU* 1.3 64.6 + - - +
96F SER 3.1 5.8 + - - -
97F PHE* 3.2 14.8 + - - +
104F TYR* 3.4 40.9 - - + +
105F ARG 3.9 11.7 - - - +
107F VAL* 4.1 22.3 + - + +
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Residues in contact with GLU 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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91F ARG* 2.8 26.4 + - + +
92F THR* 3.9 6.5 - - - +
94F THR* 1.3 69.8 - - - +
96F SER* 1.3 63.9 + - - +
97F PHE 3.1 2.7 - - - -
98F ALA* 3.0 37.3 + - - +
99F SER 4.6 0.5 + - - -
104F TYR* 4.2 14.2 + - - -
474F LYS* 5.3 2.9 + - - -
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Residues in contact with SER 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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61F LYS* 3.7 29.0 - - - +
92F THR 3.0 15.9 + - - -
93F ALA 2.9 17.9 + - - -
94F THR 3.1 0.6 - - - -
95F GLU* 1.3 77.0 - - - +
97F PHE* 1.3 74.4 + - - +
98F ALA 3.4 0.6 + - - -
99F SER* 4.6 9.4 + - - -
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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