Contacts of the helix formed by residues 83 - 96 (chain 2) in PDB entry 1ILN
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 83 (chain 2).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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712 ASN* 2.6 70.9 + - - +
722 LEU* 4.6 9.5 + - - +
752 SER* 4.7 9.8 + - - -
812 ARG* 3.0 15.7 + - + +
822 PRO* 1.4 85.4 - - - +
842 ASP* 1.3 60.2 + - - +
862 ILE* 3.3 6.6 + - - +
872 SER* 2.7 37.6 + - - +
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Residues in contact with ASP 84 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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802 LEU* 3.3 27.8 - - + +
812 ARG* 2.6 50.4 + - - +
832 ARG* 1.3 77.3 - - - +
852 LEU* 1.3 60.3 + - - +
872 SER* 3.4 8.6 - - - -
882 ASN* 2.7 37.7 + - - +
15B ARG* 2.8 34.0 + - - +
64B LEU* 5.3 0.2 - - - +
68B ASP* 4.4 1.7 - - - +
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Residues in contact with LEU 85 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202 ASP* 3.4 12.8 - - - +
232 MET* 3.5 21.1 - - + -
242 ILE* 3.7 24.5 - - + +
782 PHE* 3.4 39.5 - - + -
802 LEU* 4.2 7.0 - - + -
812 ARG 4.0 3.6 - - - +
822 PRO* 2.9 17.1 + - + +
842 ASP* 1.3 75.3 - - - +
862 ILE* 1.4 60.0 + - + +
892 ILE* 2.8 52.1 + - + +
134B TYR* 3.2 27.6 - - - +
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Residues in contact with ILE 86 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 ILE* 5.2 12.8 - - + -
632 LEU* 4.4 19.9 - - + +
672 GLU* 3.8 50.7 - - + +
702 LEU* 6.1 0.4 - - + -
712 ASN* 3.6 36.3 - - + +
822 PRO 3.1 6.1 + - - +
832 ARG 3.6 6.3 - - - +
852 LEU* 1.4 77.9 - - - +
872 SER* 1.3 57.5 + - - +
892 ILE* 4.6 4.3 - - + -
902 ASN* 2.8 41.7 + - + +
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Residues in contact with SER 87 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832 ARG* 2.7 26.3 + - - +
842 ASP* 3.4 7.8 - - - -
852 LEU 3.1 0.2 - - - -
862 ILE* 1.3 75.9 - - - +
882 ASN* 1.3 55.9 + - - +
902 ASN* 4.9 0.4 - - - -
912 VAL* 2.7 49.3 + - - +
68B ASP* 3.3 26.6 + - - -
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Residues in contact with ASN 88 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162 HIS* 4.1 15.1 + - + -
172 LEU* 4.9 0.2 - - - -
202 ASP* 2.8 41.4 + - - +
842 ASP* 2.7 25.6 + - - +
872 SER* 1.3 73.8 - - - +
892 ILE* 1.3 59.3 + - - +
912 VAL* 4.9 2.0 - - - -
922 ILE* 2.8 40.2 + - + +
15B ARG* 2.6 38.6 + - - +
68B ASP* 3.1 10.0 - - - +
134B TYR* 4.1 5.3 + - - -
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Residues in contact with ILE 89 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172 LEU* 3.6 20.4 - - + -
202 ASP* 3.4 39.0 - - + +
212 LEU* 4.1 10.5 - - + -
242 ILE* 3.8 18.8 - - + -
592 LEU* 3.8 27.4 - - + -
632 LEU* 3.9 15.5 - - + -
852 LEU* 2.8 37.6 + - + +
862 ILE* 4.1 5.6 - - + +
882 ASN* 1.3 74.1 - - - +
902 ASN* 1.4 58.0 + - - +
932 VAL* 2.8 35.7 + - - +
1182 LEU* 6.0 0.7 - - + -
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Residues in contact with ASN 90 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592 LEU* 6.1 0.7 - - - -
602 GLU* 5.5 13.9 + - - +
632 LEU* 5.3 6.3 - - + +
672 GLU* 5.9 1.4 + - - -
862 ILE* 2.8 29.7 + - + +
872 SER* 3.8 1.8 - - - +
892 ILE* 1.4 76.3 - - - +
912 VAL* 1.3 62.8 + - + +
932 VAL* 3.6 4.8 - - - +
942 LEU* 2.8 59.9 + - - +
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Residues in contact with VAL 91 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872 SER* 2.7 32.7 + - - +
882 ASN* 4.4 1.6 - - - +
902 ASN* 1.3 84.7 - - + +
922 ILE* 1.4 50.9 + - - +
942 LEU* 3.1 12.5 - - + +
68B ASP 4.3 9.6 - - - +
69B SER* 3.7 26.7 - - - +
70B GLN 4.0 14.8 - - - +
71B LYS* 2.4 45.3 + - + +
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Residues in contact with ILE 92 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132 GLN* 3.2 34.1 - - + +
162 HIS* 3.7 16.6 - - + -
172 LEU* 3.6 34.8 - - + -
882 ASN* 2.8 30.1 + - + +
912 VAL* 1.4 70.4 - - - +
932 VAL* 1.3 68.7 + - - +
942 LEU 3.0 0.9 - - - -
952 GLU* 2.9 15.8 + - + +
962 LEU* 2.9 24.7 + - + +
91B ARG* 3.2 37.7 - - - +
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Residues in contact with VAL 93 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172 LEU* 3.7 22.2 - - + -
562 LEU* 3.9 23.3 - - + +
592 LEU* 3.7 34.3 - - + -
602 GLU* 3.8 28.9 - - + -
892 ILE 2.8 26.8 + - - +
902 ASN* 3.6 4.9 - - - +
922 ILE* 1.3 75.1 - - - +
942 LEU* 1.3 56.5 + - - +
962 LEU* 4.3 6.7 - - + -
972 LYS* 2.7 39.5 + - + +
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Residues in contact with LEU 94 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602 GLU* 3.1 27.4 - - + +
902 ASN* 2.8 39.1 + - - +
912 VAL* 3.5 13.7 - - + +
932 VAL* 1.3 70.4 - - - +
952 GLU* 1.3 54.2 + - - +
972 LYS* 3.7 20.0 - - - +
71B LYS* 2.6 34.8 + - - +
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Residues in contact with GLU 95 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92 LYS* 2.6 32.8 + - - +
132 GLN* 3.6 14.3 - - + +
912 VAL 4.0 0.3 - - - +
922 ILE* 2.9 20.8 + - + +
932 VAL 2.9 3.4 + - - -
942 LEU* 1.3 71.4 - - - +
962 LEU* 1.3 59.8 + - - +
972 LYS 3.5 8.1 + - - +
982 GLY* 5.3 0.2 - - - -
71B LYS* 2.7 51.2 + - + +
72B LEU* 5.8 1.4 - - - +
91B ARG* 2.7 40.1 + - - -
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Residues in contact with LEU 96 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92 LYS* 4.1 5.8 + - - +
102 THR 3.4 25.6 - - - +
132 GLN* 3.5 15.3 - - + -
142 LEU* 3.5 17.7 - - + +
172 LEU* 3.4 44.9 - - + -
532 LEU* 3.2 42.6 - - + +
562 LEU* 3.6 15.0 - - + -
922 ILE* 2.9 23.8 + - + +
932 VAL* 4.0 1.6 - - - +
952 GLU* 1.3 75.6 - - - +
972 LYS* 1.3 64.3 + - - +
982 GLY* 3.1 5.0 + - - -
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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