Contacts of the helix formed by residues 82 - 95 (chain A) in PDB entry 2ILU
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 ARG 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A GLY 3.3 12.7 + - - +
79A ILE 3.1 6.9 + - - +
80A ARG 3.0 0.6 - - - -
81A GLU* 1.3 86.7 - - + +
83A ALA* 1.3 63.6 + - - +
84A SER* 3.4 3.4 - - - -
85A GLU* 3.3 41.0 + - + +
86A ILE* 3.0 30.1 + - + +
187A ALA* 3.4 30.7 + - - +
190A LYS* 3.4 25.3 - - - +
191A ILE* 3.7 11.7 - - - +
194A GLU* 2.5 36.1 + - - -
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Residues in contact with ALA 83 (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 ILE 2.9 9.0 + - - +
80A ARG* 3.1 17.9 + - - +
81A GLU 3.6 0.6 - - - -
82A ARG* 1.3 75.9 - - - +
84A SER* 1.3 51.9 + - - +
86A ILE* 3.2 1.9 + - - +
87A SER* 2.7 41.4 + - - +
102A GLU* 6.1 0.7 - - - +
105A VAL* 3.7 21.4 - - + +
106A ALA* 6.4 0.4 - - - -
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Residues in contact with SER 84 (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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82A ARG* 4.9 1.7 - - - -
83A ALA* 1.3 77.5 - - - +
85A GLU* 1.3 69.2 + - - +
87A SER* 3.7 7.0 - - - -
88A ALA* 2.9 27.0 + - - +
102A GLU* 6.1 1.6 - - - -
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Residues in contact with GLU 85 (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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82A ARG* 3.3 49.2 + - + +
84A SER* 1.3 84.2 + - - +
86A ILE* 1.3 64.8 + - + +
88A ALA* 3.6 5.4 + - - +
89A LEU* 3.2 34.3 + - + +
187A ALA* 5.7 2.1 - - - +
190A LYS* 5.8 2.9 + - - +
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Residues in contact with ILE 86 (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 ILE* 4.2 10.3 - - + +
82A ARG* 3.0 24.8 + - + +
83A ALA 3.7 2.5 - - - +
85A GLU* 1.3 77.1 - - + +
87A SER* 1.3 65.0 + - - +
89A LEU* 3.2 9.7 + - + +
90A ILE* 3.0 23.7 + - + +
105A VAL* 3.5 20.4 - - + -
156A PHE* 3.8 42.0 - - + -
184A ASN* 4.8 4.0 - - + -
187A ALA* 4.0 20.2 - - + -
191A ILE* 3.7 29.6 - - + -
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Residues in contact with SER 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 ALA* 2.7 30.9 + - - +
84A SER* 3.7 7.1 - - - -
86A ILE* 1.3 73.4 - - - +
88A ALA* 1.3 51.6 + - - +
90A ILE* 3.0 6.8 + - - +
91A VAL* 2.8 37.7 + - - +
101A ALA* 3.6 19.0 - - - +
102A GLU* 3.6 25.9 - - - +
105A VAL* 3.4 17.3 - - - +
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Residues in contact with ALA 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 SER 2.9 17.0 + - - +
85A GLU* 3.8 6.1 - - - +
87A SER* 1.3 76.2 - - - +
89A LEU* 1.3 57.8 + - + +
91A VAL* 3.7 9.1 - - - +
92A GLU* 2.8 31.5 + - - +
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Residues in contact with LEU 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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85A GLU* 3.2 26.0 + - + +
86A ILE* 3.2 11.4 + - - +
87A SER 3.1 0.6 - - - -
88A ALA* 1.3 74.2 - - + +
90A ILE* 1.3 66.7 + - - +
92A GLU* 3.6 18.5 - - - +
93A GLU* 3.0 32.0 + - - +
183A ASN* 4.3 28.3 - - + +
184A ASN* 4.5 6.1 - - - +
187A ALA* 3.8 29.2 - - + -
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Residues in contact with ILE 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 ILE* 3.0 9.8 + - + +
87A SER* 3.0 7.3 + - - +
89A LEU* 1.3 76.8 - - - +
91A VAL* 1.3 56.2 + - - +
93A GLU* 4.6 5.8 - - - -
94A GLY* 2.7 37.0 + - - -
95A GLY 3.6 0.3 + - - -
96A LYS* 3.8 30.6 - - + +
101A ALA* 4.2 7.9 - - + +
104A GLU* 3.9 17.0 - - - +
105A VAL* 3.7 27.1 - - + -
155A PRO* 5.1 9.6 - - + -
156A PHE* 3.6 26.9 - - + -
184A ASN* 4.1 18.4 - - + +
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Residues in contact with VAL 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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28A ASN* 5.3 0.2 - - - +
87A SER* 2.8 25.5 + - - +
88A ALA* 3.7 8.7 - - - +
90A ILE* 1.3 72.9 - - - +
92A GLU* 1.3 57.8 + - - +
95A GLY* 2.7 31.5 + - - -
96A LYS* 3.4 15.9 - - - +
98A GLN* 3.9 18.8 - - + -
101A ALA* 3.4 19.7 - - + -
317A PRO* 3.4 30.7 - - + +
318A ALA* 3.8 20.6 - - + +
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Residues in contact with GLU 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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28A ASN* 3.1 43.5 + - - +
29A PRO* 3.4 4.3 - - - +
35A ILE* 3.4 41.7 - - + +
88A ALA 2.8 22.0 + - - +
89A LEU* 3.6 22.5 - - - +
91A VAL* 1.3 78.4 - - - +
93A GLU* 1.3 59.8 + - - +
95A GLY 4.1 0.2 + - - -
183A ASN* 4.2 5.0 + - - -
318A ALA* 6.1 2.2 - - - -
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Residues in contact with GLU 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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26A VAL* 4.5 0.9 - - + -
27A VAL 4.1 1.7 - - - +
29A PRO* 3.2 17.6 - - - +
35A ILE* 3.6 22.9 - - + -
89A LEU 3.0 17.2 + - - +
90A ILE* 4.2 1.6 - - - +
92A GLU* 1.3 77.7 - - - +
94A GLY* 1.3 62.7 + - - +
95A GLY 3.4 0.2 - - - -
155A PRO* 6.1 0.2 - - + -
180A PHE 4.0 9.7 - - - +
181A THR* 2.8 44.3 - - + +
182A PRO* 3.0 5.4 - - - +
183A ASN* 2.9 23.4 + - - +
184A ASN* 2.9 37.1 + - - +
329A ILE* 3.8 12.0 - - - +
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Residues in contact with GLY 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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29A PRO* 3.9 5.2 - - - +
90A ILE* 2.7 21.9 + - - -
93A GLU* 1.3 75.0 - - - +
95A GLY* 1.3 64.0 + - - +
96A LYS* 3.3 6.4 + - - +
152A TRP* 5.2 6.3 - - - -
155A PRO* 6.2 1.6 - - - -
181A THR* 4.2 13.2 - - - -
280A ASN* 4.8 6.8 + - - -
283A GLN* 5.1 3.8 + - - +
327A PRO 4.6 5.2 - - - +
329A ILE* 4.3 13.3 + - - +
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Residues in contact with GLY 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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28A ASN* 5.6 0.7 - - - -
29A PRO* 3.6 17.0 - - - +
30A ALA* 5.5 0.4 - - - -
91A VAL 2.7 18.3 + - - -
92A GLU 4.6 0.2 - - - -
93A GLU 3.4 2.0 - - - -
94A GLY* 1.3 79.3 - - - +
96A LYS* 1.3 57.1 + - - +
280A ASN* 4.7 2.5 - - - +
317A PRO* 3.6 12.1 - - - -
326A GLY* 3.3 26.5 + - - -
327A PRO* 3.5 11.9 - - - +
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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