Contacts of the helix formed by residues 86 - 97 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A VAL* 5.6 0.7 - - + -
81A GLY 3.7 18.6 - - - +
82A ILE* 3.7 5.2 - - - -
83A GLY 2.9 12.5 + - - +
84A GLY 3.1 1.8 + - - -
85A SER* 1.3 80.8 - - - +
87A LEU* 1.3 86.9 + - + +
88A GLY 3.5 2.0 + - - -
89A ALA* 3.6 7.4 + - - +
90A ARG* 2.9 55.7 + - + +
116A PHE* 3.6 44.7 - + + -
119A GLN* 3.7 33.3 + - + +
280A TYR* 3.7 10.2 + + - -
309B THR* 4.0 15.2 - - + +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A GLY* 2.9 20.6 + - - +
84A GLY* 5.5 0.7 - - - -
86A TYR* 1.3 98.7 - - + +
88A GLY* 1.3 61.2 + - - +
90A ARG* 3.4 3.3 + - - +
91A ALA* 2.8 31.5 + - - +
280A TYR* 4.1 14.7 - - + +
283A GLU* 3.4 44.6 - - + +
284A TRP* 4.1 15.1 - - + +
287A GLN* 3.4 27.6 - - + +
309B THR* 5.8 2.2 - - + -
310B ASP* 6.0 1.8 - - - +
313B SER* 4.1 12.8 - - - -
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Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A GLY* 4.6 8.7 + - - -
86A TYR 3.5 0.4 - - - -
87A LEU* 1.3 76.7 - - - +
89A ALA* 1.3 62.6 + - - +
91A ALA* 3.3 3.9 + - - +
92A ALA* 3.1 24.6 + - - +
211A VAL* 3.6 25.9 - - - +
284A TRP* 3.6 23.4 - - - -
394A PHE* 4.1 1.9 - - - -
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Residues in contact with ALA 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A VAL* 5.7 2.0 - - + -
85A SER 5.7 2.0 - - - +
86A TYR* 3.6 10.0 + - - +
87A LEU 3.3 0.4 - - - -
88A GLY* 1.3 74.7 - - - +
90A ARG* 1.3 62.4 + - - +
92A ALA* 3.3 2.1 + - - +
93A ILE* 3.0 32.9 + - + +
116A PHE* 4.6 7.2 - - + -
143A ILE* 6.0 0.4 - - + -
211A VAL* 4.1 2.0 - - - +
215A VAL* 4.5 3.9 - - + +
216A GLY* 4.2 13.6 - - - +
219A PRO* 4.2 30.1 - - + -
220A ILE* 4.3 12.1 - - - -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TYR* 2.9 48.6 + - + +
87A LEU* 4.0 2.9 - - - +
89A ALA* 1.3 79.0 - - - +
91A ALA* 1.3 64.3 + - - +
93A ILE* 4.5 1.8 - - + -
94A GLU* 2.8 53.8 + - + +
116A PHE* 3.6 39.4 - - + -
119A GLN* 4.6 6.3 - - - +
125A TYR* 5.4 2.4 + - - -
280A TYR* 3.4 41.8 + - + +
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Residues in contact with ALA 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU 2.8 18.2 + - - +
88A GLY* 3.5 6.5 - - - +
89A ALA 3.2 0.2 - - - -
90A ARG* 1.3 77.5 - - - +
92A ALA* 1.3 57.6 + - - +
94A GLU* 4.4 0.5 - - - +
95A MSE 3.0 34.2 + - - +
277A ALA 4.6 1.6 - - - +
280A TYR* 3.7 14.7 - - - +
281A PHE* 3.6 35.5 + - + +
284A TRP* 4.3 8.3 - - + -
394A PHE* 4.3 4.7 - - + -
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Residues in contact with ALA 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88A GLY 3.1 8.3 + - - +
91A ALA* 1.3 74.8 - - - +
93A ILE* 1.3 65.6 + - - +
95A MSE 3.4 0.6 + - - -
96A LEU* 3.0 31.3 + - + +
220A ILE* 3.5 32.1 - - + -
225A LEU* 3.9 2.6 - - - +
230A MSE 4.3 6.3 - - + -
394A PHE* 3.4 37.6 - - + -
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA 3.0 24.8 + - - +
90A ARG* 4.0 4.0 - - - +
92A ALA* 1.3 75.9 - - - +
94A GLU* 1.3 65.7 + - + +
97A ASN* 2.9 47.1 + - - +
101A TYR* 4.9 11.9 - - + -
114A VAL* 3.9 33.4 - - + +
116A PHE* 4.3 8.7 - - + -
219A PRO* 3.8 29.8 - - + +
220A ILE* 4.2 9.2 - - - +
223A SER* 3.8 19.1 - - - +
225A LEU* 4.3 1.8 - - + -
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Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A ARG* 2.8 60.2 + - + +
91A ALA 4.4 0.7 - - - +
93A ILE* 1.3 80.6 - - + +
95A MSE 1.3 65.5 + - - +
96A LEU 3.4 0.3 + - - -
97A ASN* 3.7 11.5 - - - +
98A HIS 5.2 1.9 - - - +
99A SER* 5.8 1.4 - - - -
116A PHE* 5.6 0.6 - - + -
276A PRO 5.6 1.2 - - - +
277A ALA* 3.6 25.3 - - - +
279A GLN* 5.3 4.0 - - - +
280A TYR* 3.3 23.9 + - + +
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Residues in contact with MSE 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ALA 3.0 16.3 + - - +
92A ALA 3.4 3.6 + - - +
94A GLU* 1.3 78.2 - - - +
96A LEU* 1.3 75.2 + - + +
97A ASN 4.6 1.7 - - - +
277A ALA* 3.4 18.6 + - - +
278A LEU* 3.1 35.7 - - + -
281A PHE* 3.5 38.6 - - + -
389A LEU* 3.9 33.7 - - + +
393A THR* 6.5 0.7 - - - -
394A PHE* 3.7 28.3 - - + -
397A LEU* 4.8 8.1 - - + -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ALA 3.0 18.9 + - - +
95A MSE 1.3 102.2 - - + +
97A ASN* 1.3 60.6 + - - +
225A LEU* 3.7 33.6 - - + +
230A MSE 4.1 8.1 - - + -
389A LEU* 3.5 11.8 - - - +
390A ASN* 3.5 32.1 - - - +
391A GLU* 3.9 29.6 - - + +
394A PHE* 4.1 12.6 - - + -
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Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ILE* 2.9 31.4 + - - +
94A GLU* 3.7 11.4 - - - +
95A MSE 4.6 1.7 - - - +
96A LEU* 1.3 81.1 - - - +
98A HIS* 1.3 70.8 + - - +
99A SER* 3.5 2.1 + - - -
101A TYR* 3.7 28.3 - - + -
223A SER* 3.2 45.9 + - - +
225A LEU* 3.8 13.4 - - - +
277A ALA* 5.6 1.2 - - - +
128B ASP* 4.9 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