Contacts of the strand formed by residues 55 - 60 (chain 1) in PDB entry 1ILR
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 ALA 55 (chain 1).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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501 PRO* 4.0 2.8 - - - +
511 ILE* 3.0 42.5 + - + +
521 GLU 5.8 0.2 - - - +
531 PRO* 6.3 0.4 - - + -
541 HIS* 1.3 83.6 - - + +
561 LEU* 1.3 71.7 + - - +
991 ALA* 5.1 4.5 - - + -
1001 PHE 3.0 18.2 - - - +
1011 ILE* 4.4 9.6 - - + -
1141 ALA* 6.0 0.9 - - + -
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Residues in contact with LEU 56 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481 VAL* 3.9 25.8 - - + -
491 VAL 3.4 13.2 - - - +
501 PRO* 4.2 2.5 - - + -
511 ILE* 3.8 10.6 - - - +
551 ALA* 1.3 81.8 - - - +
571 PHE* 1.3 61.7 + - - +
581 LEU* 3.5 26.2 - - + -
981 PHE 3.8 0.5 - - - +
991 ALA* 3.7 3.6 - - - -
1001 PHE* 2.8 47.7 + - + +
1021 ARG* 4.1 32.5 - - + +
1111 PHE* 4.1 8.5 - - + -
1481 PHE* 4.3 12.3 - - + -
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Residues in contact with PHE 57 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471 ASP 3.6 0.5 - - - +
481 VAL* 3.4 6.8 - - - -
491 VAL* 2.9 43.9 + - + +
511 ILE* 3.5 33.2 - - + -
561 LEU* 1.3 74.8 - - - +
581 LEU* 1.3 62.4 + - - +
661 CYS* 6.3 0.2 - - + -
851 ILE* 3.9 21.7 - - + +
881 LEU* 3.7 32.5 - - + -
891 SER* 3.8 22.7 - - - -
901 GLU* 3.9 13.5 - - - -
951 ASP 3.7 22.7 - - - -
961 LYS* 5.5 0.4 - - - -
981 PHE* 3.5 25.6 - - + -
991 ALA* 3.8 9.2 - - + -
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Residues in contact with LEU 58 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461 ILE* 4.0 20.6 - - + -
471 ASP 3.5 2.0 - - - -
481 VAL* 4.0 11.4 - - + -
561 LEU* 3.5 23.6 - - + -
571 PHE* 1.3 79.1 - - - +
591 GLY* 1.3 58.0 + - - +
661 CYS* 3.4 6.7 - - - +
671 LEU* 2.9 53.9 + - + +
851 ILE* 4.3 3.4 - - - -
981 PHE* 4.4 5.1 + - - +
1001 PHE* 3.8 34.3 - - + -
1111 PHE* 4.1 26.5 - - + -
1211 LEU* 4.8 6.7 - - + -
1481 PHE* 4.3 1.1 - - + -
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Residues in contact with GLY 59 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461 ILE* 3.4 6.6 - - - +
471 ASP* 2.7 42.1 + - - -
581 LEU* 1.3 76.2 - - - +
601 ILE* 1.3 67.5 + - - +
631 GLY* 4.8 1.3 - - - -
651 MET 3.0 13.9 - - - -
661 CYS* 4.0 7.0 - - - -
671 LEU* 4.6 3.8 - - - +
801 LEU* 5.9 0.2 - - - -
851 ILE* 4.1 4.2 - - - +
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Residues in contact with ILE 60 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251 LEU* 4.0 15.3 - - + -
301 LEU* 4.3 13.7 - - + -
441 GLU* 4.2 12.6 - - + +
451 LYS 3.7 15.7 - - - +
461 ILE* 4.0 14.6 - - + -
471 ASP* 3.4 4.9 - - - -
591 GLY* 1.3 79.9 - - - +
611 HIS* 1.3 81.0 + - + +
621 GLY 3.3 3.1 - - - -
631 GLY 3.1 0.2 + - - -
641 LYS 3.0 17.8 + - - -
651 MET* 2.8 49.0 + - + +
671 LEU* 6.0 2.5 - - + -
801 LEU* 3.9 24.9 - - + -
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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