Contacts of the helix formed by residues 86 - 97 (chain C) in PDB entry 3IFS
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 86 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C VAL* 5.6 0.2 - - - -
81C GLY 3.8 7.6 - - - +
82C ILE* 3.7 14.6 - - - -
83C GLY 3.0 13.4 + - - +
84C GLY 3.2 1.0 - - - -
85C SER* 1.3 80.3 - - - +
87C LEU* 1.3 87.7 + - + +
88C GLY 3.5 1.9 + - - -
89C ALA* 3.6 6.9 + - - +
90C ARG* 2.9 57.0 + - - +
116C PHE* 3.5 46.5 - + + -
119C GLN* 3.7 34.6 + - + +
280C TYR* 3.5 12.0 + + - -
309D THR* 4.0 14.4 - - + +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C GLY* 3.0 18.1 + - - +
84C GLY* 5.6 0.2 - - - -
86C TYR* 1.3 101.2 - - + +
88C GLY* 1.3 60.6 + - - +
90C ARG* 3.8 2.5 - - - +
91C ALA* 2.8 32.6 + - - +
280C TYR* 4.0 14.6 - - + +
283C GLU* 3.6 43.5 - - + +
284C TRP* 4.2 14.1 - - + +
287C GLN* 3.4 28.9 - - + +
309D THR* 5.7 2.0 - - + -
310D ASP* 6.1 0.9 - - - +
313D SER* 4.1 12.8 - - - +
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Residues in contact with GLY 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C GLY* 4.6 8.1 + - - -
86C TYR 3.5 0.6 - - - -
87C LEU* 1.3 78.5 - - - +
89C ALA* 1.3 62.7 + - - +
91C ALA* 3.7 3.0 - - - +
92C ALA* 3.1 21.8 + - - +
211C VAL* 3.5 31.7 - - - +
284C TRP* 3.6 21.3 - - - -
394C PHE* 4.0 2.0 - - - -
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Residues in contact with ALA 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C VAL* 5.7 1.3 - - + -
84C GLY 5.7 0.2 + - - -
85C SER 5.5 2.9 - - - +
86C TYR* 3.6 10.4 + - - +
87C LEU 3.4 0.4 - - - -
88C GLY* 1.3 74.4 - - - +
90C ARG* 1.3 64.0 + - - +
92C ALA* 3.3 1.9 + - - +
93C ILE* 3.0 32.8 + - + +
116C PHE* 4.6 6.7 - - + -
143C ILE* 6.0 0.2 - - + -
211C VAL* 4.1 2.0 - - - +
215C VAL* 4.4 4.9 - - + +
216C GLY* 4.2 13.0 - - - +
219C PRO* 4.1 31.9 - - + -
220C ILE* 4.3 11.4 - - - -
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Residues in contact with ARG 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C TYR* 2.9 49.2 + - + +
87C LEU* 4.0 3.1 - - - +
89C ALA* 1.3 75.6 - - - +
91C ALA* 1.3 64.1 + - - +
93C ILE* 4.6 1.8 - - - -
94C GLU* 2.9 52.2 + - + +
116C PHE* 3.8 38.8 - - + +
119C GLN* 4.6 6.9 - - - +
125C TYR* 5.2 3.2 + - - -
280C TYR* 3.4 46.0 + - + -
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87C LEU 2.8 19.2 + - - +
88C GLY* 3.7 5.2 - - - +
89C ALA 3.3 0.2 - - - -
90C ARG* 1.3 77.1 - - - +
92C ALA* 1.3 57.3 + - - +
94C GLU* 4.1 0.7 - - - +
95C MSE 2.9 33.3 + - - +
277C ALA 4.7 1.2 - - - +
280C TYR* 3.6 15.8 - - - +
281C PHE* 3.5 37.7 + - + +
284C TRP* 4.2 7.9 - - + -
394C PHE* 4.3 4.7 - - + -
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Residues in contact with ALA 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C GLY 3.1 8.9 + - - +
89C ALA 3.8 0.2 - - - +
91C ALA* 1.3 73.6 - - - +
93C ILE* 1.3 67.2 + - - +
95C MSE 4.6 0.4 - - - -
96C LEU* 3.0 30.8 + - + +
220C ILE* 3.4 35.0 - - + -
225C LEU* 3.8 2.1 - - - +
230C MSE 4.3 8.3 - - + -
394C PHE* 3.5 31.6 - - + -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C ALA 3.0 25.3 + - - +
90C ARG* 4.0 3.8 - - - +
92C ALA* 1.3 74.0 - - - +
94C GLU* 1.3 68.4 + - + +
97C ASN* 3.0 46.7 + - + +
101C TYR* 5.0 10.5 - - + -
114C VAL* 4.0 31.0 - - + -
116C PHE* 4.3 8.3 - - + -
219C PRO* 3.7 31.4 - - + +
220C ILE* 4.1 10.5 - - + +
223C SER* 3.8 19.7 - - - +
225C LEU* 4.3 1.8 - - + -
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Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 2.9 58.3 + - + +
91C ALA 4.3 0.9 - - - +
93C ILE* 1.3 82.4 - - + +
95C MSE 1.3 64.9 + - - +
96C LEU 3.4 0.2 + - - -
97C ASN* 3.7 12.1 - - - +
98C HIS 5.1 1.5 - - - +
99C SER* 5.7 1.0 - - - -
116C PHE* 5.7 0.8 - - + -
276C PRO 5.5 1.9 - - - +
277C ALA* 3.6 24.3 - - - +
279C GLN* 5.5 3.5 - - - +
280C TYR* 3.6 23.1 + - + +
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Residues in contact with MSE 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C ALA 2.9 16.7 + - - +
92C ALA* 4.0 2.9 - - - +
94C GLU* 1.3 77.8 - - - +
96C LEU* 1.3 76.4 + - + +
97C ASN 4.6 1.6 - - - +
277C ALA* 3.5 23.8 + - - +
278C LEU* 2.9 33.7 - - + -
281C PHE* 3.6 35.0 - - + -
389C LEU* 3.9 33.9 - - + +
390C ASN 5.5 0.4 - - - +
394C PHE* 3.8 28.5 - - + -
397C LEU* 4.7 8.1 - - + -
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Residues in contact with LEU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA 3.0 17.8 + - - +
95C MSE 1.3 101.7 - - + +
97C ASN* 1.3 63.4 + - - +
225C LEU* 3.8 31.8 - - + +
230C MSE 4.1 14.1 - - + -
389C LEU* 3.7 9.9 - - + +
390C ASN* 3.6 33.0 - - - +
391C GLU* 4.0 27.6 - - + +
394C PHE* 4.1 8.5 - - + -
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Residues in contact with ASN 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ILE* 3.0 24.4 + - + +
94C GLU* 3.7 10.5 + - - +
95C MSE 3.6 1.9 - - - +
96C LEU* 1.3 82.2 + - - +
98C HIS* 1.3 71.3 + - - +
99C SER* 3.4 2.3 + - - -
101C TYR* 3.7 29.6 - - + -
223C SER* 3.1 40.7 + - - -
224C GLY 5.5 0.4 - - - -
225C LEU* 3.6 15.7 - - - +
277C ALA* 5.5 1.9 - - - +
128D ASP* 4.8 0.5 - - - +
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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