Contacts of the helix formed by residues 86 - 97 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309A THR* 4.1 14.3 - - + +
79B VAL* 5.6 0.7 - - - -
81B GLY 3.7 8.7 - - - +
82B ILE* 3.6 15.3 - - - -
83B GLY 2.9 13.4 + - - +
84B GLY 3.2 1.4 + - - -
85B SER* 1.3 79.8 - - - +
87B LEU* 1.3 91.3 + - + +
88B GLY 3.4 2.3 + - - -
89B ALA* 3.5 7.4 + - - +
90B ARG* 2.8 54.1 + - + +
116B PHE* 3.6 46.4 - + + -
119B GLN* 3.6 34.7 + - + +
280B TYR* 3.5 12.9 + + - -
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR* 5.7 2.7 - - + -
310A ASP* 6.0 1.8 - - - +
313A SER* 4.1 11.9 - - - -
83B GLY* 3.0 20.2 + - - +
84B GLY* 5.8 0.2 - - - -
86B TYR* 1.3 97.2 - - + +
88B GLY* 1.3 59.9 + - - +
90B ARG* 4.0 2.8 - - - +
91B ALA* 2.8 32.2 + - - +
280B TYR* 4.1 14.1 - - + +
283B GLU* 3.6 42.8 - - + +
284B TRP* 4.1 16.1 - - + +
287B GLN* 3.4 29.2 - - + +
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Residues in contact with GLY 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLY* 4.8 8.4 + - - -
86B TYR 3.4 0.8 - - - -
87B LEU* 1.3 77.7 - - - +
89B ALA* 1.3 63.1 + - - +
91B ALA* 3.6 3.4 - - - +
92B ALA* 3.1 21.1 + - - +
211B VAL* 3.5 31.3 - - - +
215B VAL* 6.5 0.7 - - - -
284B TRP* 3.6 20.4 - - - -
394B PHE* 4.0 2.1 - - - -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 5.7 1.6 - - + -
85B SER 5.7 2.2 - - - +
86B TYR* 3.5 9.6 + - - +
87B LEU 3.4 0.2 - - - -
88B GLY* 1.3 75.3 - - - +
90B ARG* 1.3 59.6 + - - +
92B ALA* 3.3 1.6 + - - +
93B ILE* 2.9 38.7 + - + +
116B PHE* 4.8 6.5 - - + -
143B ILE* 6.0 0.7 - - + -
211B VAL* 4.1 2.2 - - - +
215B VAL* 4.3 5.5 - - + +
216B GLY* 4.2 21.1 - - - +
219B PRO* 4.2 24.9 - - + -
220B ILE* 4.4 9.4 - - - -
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Residues in contact with ARG 90 (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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86B TYR* 2.8 55.5 + - + +
87B LEU 4.0 2.7 - - - +
89B ALA* 1.3 77.4 - - - +
91B ALA* 1.3 61.7 + - - +
93B ILE* 3.9 2.0 - - + -
94B GLU* 3.0 52.0 + - + +
116B PHE* 3.7 41.2 - - + +
119B GLN* 4.4 7.9 - - - +
125B TYR* 5.2 2.4 + - - -
280B TYR* 3.4 45.1 + - + -
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Residues in contact with ALA 91 (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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87B LEU 2.8 23.2 + - - +
88B GLY* 3.6 5.6 - - - +
90B ARG* 1.3 73.3 - - - +
92B ALA* 1.3 56.8 + - - +
94B GLU* 4.1 0.7 - - - +
95B MSE 3.0 34.8 + - - +
277B ALA 4.8 1.4 - - - +
280B TYR* 3.6 17.2 - - - +
281B PHE* 3.6 34.8 + - + -
284B TRP* 4.3 7.6 - - + -
394B PHE* 4.3 4.9 - - + -
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Residues in contact with ALA 92 (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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88B GLY 3.1 9.1 + - - +
91B ALA* 1.3 74.5 - - - +
93B ILE* 1.3 66.8 + - - +
95B MSE 4.5 0.2 - - - -
96B LEU* 3.0 31.8 + - + +
220B ILE* 3.5 31.6 - - + -
225B LEU* 3.8 2.1 - - - +
230B MSE 4.5 6.1 - - + -
394B PHE* 3.5 36.1 - - + -
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Residues in contact with ILE 93 (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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89B ALA 2.9 23.5 + - - +
90B ARG* 4.0 4.3 - - - +
92B ALA* 1.3 73.9 - - - +
94B GLU* 1.3 63.5 + - + +
97B ASN* 3.0 51.6 + - + +
101B TYR* 4.9 10.3 - - + +
114B VAL* 3.8 35.0 - - + -
116B PHE* 4.4 8.1 - - + -
219B PRO* 3.6 32.1 - - + +
220B ILE* 4.2 8.5 - - + +
223B SER* 3.8 18.2 - - - +
225B LEU* 4.4 0.9 - - - -
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Residues in contact with GLU 94 (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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90B ARG* 3.0 52.9 + - + +
91B ALA 4.3 1.1 - - - +
93B ILE* 1.3 81.8 - - + +
95B MSE 1.3 62.8 + - - +
97B ASN* 3.7 12.3 - - - +
98B HIS 5.1 2.2 - - - +
99B SER* 5.6 2.1 - - - -
116B PHE* 6.2 0.7 - - + -
276B PRO 5.6 1.0 - - - +
277B ALA* 3.5 26.0 - - - +
279B GLN* 5.4 2.8 - - - +
280B TYR* 3.3 31.3 + - + +
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Residues in contact with MSE 95 (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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91B ALA 3.0 21.7 + - - +
92B ALA* 3.9 2.9 - - - +
94B GLU* 1.3 76.5 - - - +
96B LEU* 1.3 74.9 + - + +
97B ASN 4.7 1.3 - - - +
277B ALA* 3.5 18.8 + - - +
278B LEU* 3.0 34.3 - - + -
281B PHE* 3.6 39.0 - - + -
389B LEU* 3.9 33.3 - - + +
390B ASN 5.6 0.2 - - - +
394B PHE* 3.7 26.5 - - + -
397B LEU* 4.6 10.5 - - + -
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Residues in contact with LEU 96 (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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92B ALA 3.0 15.2 + - - +
95B MSE 1.3 100.1 - - + +
97B ASN* 1.3 61.5 + - - +
225B LEU* 3.7 36.4 - - + +
230B MSE 3.9 22.2 - - + -
389B LEU 3.7 9.2 - - - +
390B ASN* 3.6 34.8 - - - +
391B GLU* 4.0 17.5 - - + +
394B PHE* 4.0 9.6 - - + -
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Residues in contact with ASN 97 (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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128A ASP* 4.9 0.3 - - - +
93B ILE* 3.0 27.4 + - + +
94B GLU* 3.7 11.0 - - - +
95B MSE 4.7 1.4 - - - +
96B LEU* 1.3 80.5 + - - +
98B HIS* 1.3 70.1 + - - +
99B SER* 3.4 2.3 + - - -
101B TYR* 3.7 28.4 - - + -
223B SER* 3.1 45.0 + - - +
224B GLY 5.5 0.2 - - - -
225B LEU* 3.7 18.0 - - - +
277B ALA* 5.5 1.6 - - - +
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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