Contacts of the helix formed by residues 57 - 72 (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 GLN 57 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542 LYS 4.1 3.2 + - - -
552 HIS 3.0 2.8 + - - +
562 LEU* 1.4 76.1 - - - +
582 CYS* 1.4 60.3 + - - +
602 GLU* 3.1 23.2 + - + +
612 GLU* 2.8 58.9 + - + +
972 LYS* 4.3 7.5 - - + +
992 SER* 6.2 0.4 - - - -
1002 GLU 5.4 0.8 + - - -
1012 THR 5.3 3.6 + - - -
1032 PHE* 2.9 33.9 + - + +
1042 MET* 3.5 8.9 - - - +
1052 CYS* 2.9 29.2 + - - +
1072 TYR* 5.2 0.7 + - - -
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Residues in contact with CYS 58 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472 PRO* 3.6 27.1 - - + -
502 ALA* 5.8 0.2 - - - -
552 HIS* 3.0 17.8 + - - +
572 GLN* 1.4 77.2 - - - +
592 LEU* 1.4 60.9 + - - +
612 GLU* 4.6 1.8 - - - -
622 GLU* 3.3 25.0 + - + +
1052 CYS* 2.0 53.6 - - - -
1062 GLU* 2.7 23.6 - - - -
1172 PHE* 3.6 7.1 - - - -
1212 TRP* 4.1 2.7 - - + -
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Residues in contact with LEU 59 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172 LEU* 4.6 3.6 - - + -
212 LEU* 4.5 12.1 - - + -
562 LEU* 2.9 29.2 + - + +
582 CYS* 1.4 76.6 - - - +
602 GLU* 1.4 62.7 + - - +
632 LEU* 2.7 52.7 + - + +
892 ILE* 3.8 23.6 - - + -
902 ASN* 6.1 0.7 - - - -
932 VAL* 3.7 26.5 - - + -
1172 PHE* 3.8 2.6 - - + -
1212 TRP* 3.7 49.8 - - + +
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Residues in contact with GLU 60 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562 LEU 3.0 15.1 + - - +
572 GLN* 3.4 20.8 - - + +
592 LEU* 1.4 81.3 - - - +
612 GLU* 1.3 56.5 - - + +
632 LEU* 3.7 5.7 - - - +
642 LYS* 3.0 30.8 + - - +
672 GLU* 5.4 0.2 - - - +
902 ASN* 5.5 13.2 + - - +
932 VAL* 3.8 16.6 - - + -
942 LEU* 3.1 20.5 - - + +
972 LYS* 2.5 47.0 + - - +
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Residues in contact with GLU 61 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572 GLN* 2.8 40.2 + - + +
582 CYS* 4.6 0.9 - - - -
602 GLU* 1.3 78.1 - - + +
622 GLU* 1.4 55.1 + - - +
642 LYS* 3.2 8.9 + - - +
652 PRO* 2.9 11.4 - - - +
1052 CYS* 4.1 2.6 - - - +
1072 TYR* 2.6 34.0 + - - -
31A LYS* 2.5 54.1 + - + +
35A ARG* 2.8 24.6 + - - -
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Residues in contact with GLU 62 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442 PHE* 4.3 6.4 - - - +
452 TYR* 3.0 50.0 - - + +
472 PRO* 5.2 3.4 - - + -
582 CYS* 3.3 23.7 + - + +
612 GLU* 1.4 78.6 - - - +
632 LEU* 1.4 63.0 + - - +
652 PRO* 3.4 16.0 - - - +
662 LEU* 3.9 8.7 - - - +
1052 CYS* 5.0 1.1 - - - -
1072 TYR* 3.3 16.4 - - + -
1172 PHE* 3.6 20.3 - - + -
31A LYS* 2.7 26.8 + - - -
35A ARG* 2.6 26.0 + - - -
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Residues in contact with LEU 63 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 ILE* 5.7 4.5 - - + -
592 LEU* 2.7 40.8 + - + +
602 GLU* 3.7 5.6 - - - +
622 GLU* 1.4 75.7 - - - +
642 LYS* 1.3 61.8 + - - +
662 LEU* 2.8 24.3 + - + +
672 GLU* 2.7 47.5 + - + +
702 LEU* 6.3 0.4 - - + -
862 ILE* 4.4 21.8 - - + -
892 ILE* 3.9 21.8 - - + -
902 ASN* 5.3 7.2 - - + +
1172 PHE* 3.5 12.7 - - + -
1182 LEU* 5.1 6.5 - - + -
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Residues in contact with LYS 64 (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 3.0 15.6 + - - +
612 GLU* 3.2 16.8 - - - +
632 LEU* 1.3 75.3 - - - +
652 PRO* 1.4 51.1 - - + +
662 LEU 3.2 2.4 + - - -
672 GLU* 2.6 45.7 + - - +
682 GLU* 2.6 46.1 + - - +
16A LYS* 2.7 26.2 + - - +
29A GLU* 3.9 13.9 - - - +
31A LYS* 4.4 11.9 - - + -
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Residues in contact with PRO 65 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442 PHE* 3.3 23.3 - - + -
452 TYR* 5.4 1.1 - - + -
612 GLU 2.9 25.6 - - - +
622 GLU* 3.4 23.1 - - - +
642 LYS* 1.4 79.6 - - + +
662 LEU* 1.3 53.3 + - - -
692 VAL* 3.8 1.2 - - - +
14A THR* 3.3 25.2 - - + +
16A LYS* 3.6 14.1 - - - +
29A GLU* 4.4 1.1 - - - +
31A LYS* 3.3 42.2 - - + +
32A ARG* 4.3 8.7 - - + +
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Residues in contact with LEU 66 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 ILE* 5.5 0.2 - - + -
442 PHE* 3.6 24.2 - - + -
622 GLU 3.9 4.9 - - - +
632 LEU* 3.1 23.8 - - + +
652 PRO* 1.3 74.9 - - - +
672 GLU* 1.3 58.7 + - - +
682 GLU 3.4 1.8 - - - -
692 VAL* 2.8 30.5 + - + +
702 LEU* 2.8 50.7 + - + -
1142 ILE* 3.5 27.4 - - + +
1172 PHE* 3.7 33.0 - - + -
1182 LEU* 4.2 8.1 - - + -
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Residues in contact with GLU 67 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602 GLU 5.4 0.3 - - - +
632 LEU* 2.7 24.8 + - + +
642 LYS* 2.6 45.1 + - - +
662 LEU* 1.3 72.0 - - - +
682 GLU* 1.3 69.6 + - + +
702 LEU* 3.1 1.2 + - - -
712 ASN* 2.7 39.8 + - + +
862 ILE* 3.8 44.1 - - + +
902 ASN* 5.9 1.4 + - - -
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Residues in contact with GLU 68 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642 LYS* 2.6 41.6 + - - +
662 LEU 3.4 0.6 - - - -
672 GLU* 1.3 85.9 - - - +
692 VAL* 1.3 57.3 + - - +
712 ASN* 4.2 8.7 - - - +
722 LEU* 2.8 31.9 + - - +
16A LYS* 2.5 65.9 + - + +
29A GLU* 4.2 2.3 - - - +
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Residues in contact with VAL 69 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392 MET* 3.4 40.7 - - + +
422 PHE* 6.2 2.5 - - + -
442 PHE* 5.2 4.7 - - + -
652 PRO 3.8 8.1 - - - +
662 LEU* 2.8 17.0 + - + +
682 GLU* 1.3 77.2 - - - +
702 LEU* 1.3 61.1 + - + +
712 ASN 3.1 0.4 - - - -
722 LEU* 3.2 6.5 + - - +
732 ALA* 2.9 25.5 + - - +
6A ASP* 5.3 2.9 - - - +
14A THR* 3.1 42.0 - - + +
15A PHE* 4.7 7.6 - - + +
16A LYS* 3.8 15.3 - - + +
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Residues in contact with LEU 70 (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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242 ILE* 4.1 10.6 - - + +
282 ILE* 3.4 44.3 - - + +
332 ASN* 5.6 0.4 - - - +
392 MET* 3.7 25.8 - - + -
632 LEU* 6.3 0.4 - - + -
662 LEU* 2.8 55.0 + - + +
672 GLU* 4.3 2.2 - - - +
692 VAL* 1.3 76.8 - - + +
712 ASN* 1.3 59.4 + - - +
732 ALA* 3.4 16.6 - - + +
782 PHE* 3.6 8.5 - - - -
822 PRO* 4.1 1.4 - - - +
862 ILE* 5.7 1.8 - - + -
1142 ILE* 4.4 20.6 - - + -
1182 LEU* 4.1 14.6 - - + -
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Residues in contact with ASN 71 (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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672 GLU* 2.7 21.9 + - - +
682 GLU* 4.0 7.5 - - - +
702 LEU* 1.3 77.4 - - - +
722 LEU* 1.4 64.2 + - - +
732 ALA 3.2 2.5 - - - +
822 PRO* 3.0 31.2 - - - +
832 ARG* 2.6 64.7 + - - +
862 ILE* 3.6 27.1 - - + +
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Residues in contact with LEU 72 (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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352 LYS* 3.6 28.5 - - + -
392 MET* 5.3 2.9 - - + -
682 GLU 2.8 19.8 + - - +
692 VAL* 3.4 5.6 - - - +
712 ASN* 1.4 74.1 - - - +
732 ALA* 1.4 69.2 + - - +
742 GLN* 3.1 8.1 + - - -
752 SER 4.6 0.7 + - - -
832 ARG* 4.6 10.9 + - - +
15A PHE 4.0 2.2 - - - +
16A LYS 3.4 12.6 - - - +
17A ALA* 4.0 2.9 - - - -
18A MET* 3.2 51.6 - - + +
20A TYR* 6.4 1.1 - - + -
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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