Contacts of the helix formed by residues 75 - 88 (chain B) in PDB entry 4IF8
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 SER 75 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LEU* 1.3 78.0 - - - +
76B PRO* 1.4 64.6 - - - +
77B LEU* 3.7 2.6 + - - +
78B SER* 3.0 22.8 + - - -
79B ILE* 3.1 24.6 + - - +
208B ILE* 3.4 33.7 - - - +
354B HIS* 3.2 6.5 + - - -
356B ALA* 4.0 0.2 - - - +
403B LEU 2.6 23.4 + - - -
404B PHE* 4.2 1.6 - - - -
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Residues in contact with PRO 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 3.3 25.4 - - + +
55B LEU* 3.9 9.9 - - + +
56B GLY* 3.7 25.6 - - - +
59B LEU* 5.5 0.4 - - + -
74B LEU* 3.7 15.2 - - + +
75B SER* 1.4 83.2 - - - +
77B LEU* 1.4 55.1 + - - +
79B ILE* 3.6 3.2 + - + +
80B SER* 2.9 34.6 + - - -
402B VAL* 3.4 33.7 - - + +
404B PHE* 4.0 1.6 - - - -
405B LEU* 3.9 15.3 - - + +
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Residues in contact with LEU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 3.6 24.2 - - - +
75B SER* 3.3 3.1 - - - +
76B PRO* 1.4 75.8 - - - +
78B SER* 1.4 56.2 + - - +
80B SER* 3.2 4.0 + - - -
81B THR* 2.9 49.6 + - + +
116B PHE* 3.9 11.0 - - + -
119B ILE* 3.7 21.8 - - + -
123B LEU* 3.7 17.3 - - + -
134B ILE* 3.8 18.4 - - + -
208B ILE* 5.2 2.0 - - + -
401B SER* 3.8 5.6 - - - +
402B VAL 3.2 22.0 + - - +
403B LEU* 3.7 27.6 - - + -
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Residues in contact with SER 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B SER* 3.0 27.7 + - - -
77B LEU* 1.4 77.0 - - - +
79B ILE* 1.3 62.7 + - - +
81B THR* 2.7 25.6 + - - -
82B ALA 3.3 1.2 + - - -
134B ILE* 3.6 15.4 - - - +
206B ASN* 2.7 39.6 + - - -
207B TYR 3.7 8.5 + - - -
208B ILE* 3.7 12.3 - - - +
354B HIS* 3.8 4.5 - - - -
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Residues in contact with ILE 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.9 0.9 - - + -
59B LEU* 4.0 17.7 - - + -
74B LEU* 4.0 24.2 - - + -
75B SER 3.1 19.5 + - - +
76B PRO* 4.0 3.6 - - + +
78B SER* 1.3 74.1 - - - +
80B SER* 1.4 62.5 + - - +
82B ALA* 3.2 17.1 + - - +
83B PHE* 3.3 16.9 + - + -
102B PHE* 3.8 23.8 - - + -
206B ASN* 4.3 3.6 - - - -
317B PHE* 6.0 0.4 - - + -
319B LEU* 4.0 25.1 - - + -
322B THR* 5.5 1.8 - - + -
323B LEU* 4.3 6.1 - - + -
354B HIS* 3.7 35.9 - - + +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 3.8 11.7 - - - +
55B LEU* 3.3 17.7 - - - +
76B PRO 2.9 18.3 + - - -
77B LEU* 3.2 7.4 + - - -
79B ILE* 1.4 75.5 - - - +
81B THR* 1.4 55.8 + - - +
83B PHE 3.3 0.9 + - - -
84B SER* 2.9 32.2 + - - -
102B PHE* 3.7 14.8 + - - -
104B PHE* 3.6 10.2 - - - -
116B PHE* 3.7 22.7 - - - -
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Residues in contact with THR 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 2.9 32.3 + - + +
78B SER* 2.7 19.3 + - - -
80B SER* 1.4 74.4 - - - +
82B ALA* 1.3 55.0 + - - +
84B SER* 4.6 0.2 - - - -
85B MET* 2.9 31.2 + - - +
116B PHE* 3.8 25.8 - - + -
120B ILE* 3.8 26.7 - - + -
134B ILE* 3.7 8.8 - - + +
136B ASN* 3.0 22.5 + - - -
158B TYR* 3.5 6.3 - - - -
206B ASN* 3.7 1.4 + - - -
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Residues in contact with ALA 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B SER 4.0 0.2 - - - +
79B ILE* 3.2 12.0 + - - +
81B THR* 1.3 80.5 + - - +
83B PHE* 1.4 63.7 + - + +
85B MET* 3.5 8.6 + - - +
86B LEU* 3.1 29.9 + - - +
136B ASN* 3.3 23.8 - - - +
204B LEU* 3.8 22.6 - - + +
206B ASN* 3.8 15.5 - - + +
319B LEU* 5.3 0.2 - - + -
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Residues in contact with PHE 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE* 3.3 17.9 + - + -
80B SER 3.3 0.6 + - - +
82B ALA* 1.4 75.5 - - + +
84B SER* 1.3 64.3 + - - +
86B LEU* 3.4 24.2 + - + +
87B CYS* 3.2 25.6 + - - -
98B ILE* 3.7 14.8 - - + +
102B PHE* 3.7 35.9 - + + -
104B PHE* 4.2 3.4 - - - -
204B LEU* 4.0 16.8 - - + -
319B LEU* 3.8 27.8 - - + -
323B LEU* 3.4 27.8 - - + -
328B VAL* 5.1 0.2 - - + -
331B ILE* 4.0 15.5 - - + -
332B PHE* 3.7 24.7 - + - -
352B ALA* 4.4 0.4 - - + -
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B SER 2.9 18.5 + - - -
81B THR 4.0 2.2 - - - -
83B PHE* 1.3 72.8 - - - +
85B MET* 1.3 68.0 + - - +
87B CYS* 3.0 21.5 + - - +
104B PHE* 3.7 12.9 - - - -
112B LEU* 3.2 17.3 - - - +
113B HIS* 3.3 9.9 - - - -
116B PHE* 3.2 28.0 - - - -
158B TYR* 2.7 22.6 + - - -
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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
----------------------------------------------------------
81B THR 2.9 19.6 + - - +
82B ALA* 3.5 12.3 - - - +
83B PHE 3.3 0.2 - - - -
84B SER* 1.3 75.9 - - - +
86B LEU* 1.3 70.8 + - + +
88B LEU* 3.1 24.3 + - - +
136B ASN* 4.6 8.1 - - + -
138B LEU* 4.7 11.0 - - + -
150B PHE* 3.8 25.5 - - - -
154B ALA* 4.0 17.9 - - + -
158B TYR* 3.7 39.1 - - + -
160B ALA* 4.1 14.8 - - + -
204B LEU* 3.9 24.7 - - + -
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Residues in contact with LEU 86 (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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82B ALA 3.1 13.6 + - - +
83B PHE* 3.7 40.2 - - + +
84B SER 3.2 0.4 - - - -
85B MET* 1.3 84.1 - - + +
87B CYS* 1.4 55.5 + - - +
89B GLY* 2.9 21.2 + - - +
90B ALA* 3.2 13.5 + - - +
98B ILE* 4.6 2.9 - - + -
138B LEU* 4.1 34.1 - - + -
150B PHE* 4.7 1.9 - - + -
204B LEU* 3.8 16.8 - - + -
331B ILE* 4.0 23.1 - - + -
338B LEU* 5.1 0.2 - - - +
341B ILE* 4.3 15.7 - - + +
349B VAL* 4.1 13.7 - - + -
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Residues in contact with CYS 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 PHE 3.2 18.9 + - - -
84B SER* 3.0 17.7 + - - +
86B LEU* 1.4 74.1 - - - +
88B LEU* 1.4 60.7 + - - +
89B GLY 3.3 0.7 + - - -
90B ALA* 3.4 18.4 + - - +
95B LEU* 3.7 28.2 - - + +
98B ILE* 3.6 26.2 - - - -
99B LYS* 4.6 8.3 - - - -
104B PHE* 4.4 9.0 - - - -
109B GLU* 4.4 9.2 - - + +
112B LEU* 4.5 6.5 - - + -
113B HIS* 4.2 11.8 + - + +
340B LYS* 4.5 1.7 + - - -
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Residues in contact with LEU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B SER 3.7 0.8 + - - -
85B MET 3.1 19.8 + - - +
87B CYS* 1.4 76.3 - - - +
89B GLY* 1.3 56.6 + - - +
113B HIS* 3.5 39.2 - - + +
150B PHE* 3.8 16.1 - - + +
153B ASP* 3.7 27.3 - - + +
154B ALA* 3.6 38.4 - - + +
157B PHE* 4.6 5.4 - - + -
158B TYR* 3.9 13.7 - - + -
340B LYS* 3.4 22.2 + - - +
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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
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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