Contacts of the helix formed by residues 498 - 508 (chain E) in PDB entry 5IIO
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 GLU 498 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469E GLN* 4.6 14.8 + - - +
470E GLN* 2.9 35.3 + - - +
494E VAL* 4.6 1.6 - - + -
495E PRO* 2.9 30.1 + - + +
497E SER* 1.3 86.1 - - - +
499E PHE* 1.3 56.7 + - - +
500E ALA 3.4 2.7 - - - -
501E CYS* 3.4 4.3 + - - +
502E ALA* 2.8 29.7 + - - +
529E GLU 3.8 0.9 - - - +
530E HIS* 2.9 43.8 + - - +
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Residues in contact with PHE 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411E LEU* 4.2 19.1 - - + -
413E VAL* 3.9 24.9 - - + -
431E LEU* 3.6 35.4 - - + -
433E THR* 3.5 33.9 - - + -
494E VAL* 4.2 7.6 - - + -
495E PRO 3.4 2.2 + - - +
496E TYR* 3.0 31.2 + + + +
497E SER 3.5 0.6 - - - -
498E GLU* 1.3 74.8 - - - +
500E ALA* 1.3 61.8 + - - +
502E ALA* 4.3 0.2 - - - -
503E LEU* 2.8 55.7 + - + +
554E PRO 5.6 5.4 - - - +
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Residues in contact with ALA 500 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496E TYR 4.7 0.6 + - - -
498E GLU 3.4 0.6 - - - -
499E PHE* 1.3 79.7 - - - +
501E CYS* 1.3 65.0 + - - +
503E LEU* 3.6 7.8 - - - +
504E LEU* 3.0 23.0 + - - +
553E THR* 3.2 31.2 + - - +
554E PRO 3.9 3.6 + - - +
555E THR* 3.4 33.7 - - - +
556E GLU* 3.6 10.7 - - - +
559E VAL* 4.6 2.7 - - + -
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Residues in contact with CYS 501 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497E SER 6.2 0.2 - - - -
498E GLU* 3.4 3.6 + - - +
499E PHE 3.3 0.4 - - - -
500E ALA* 1.3 79.8 - - - +
502E ALA* 1.3 62.7 + - - +
504E LEU* 3.3 7.2 + - - +
505E TYR* 3.0 24.6 + - - +
527E LEU* 3.9 13.2 - - - +
528E SER 3.6 15.4 - - - +
529E GLU* 3.5 4.4 - - - -
530E HIS 3.6 8.5 - - - +
531E ALA* 3.5 16.2 - - - +
532E LEU 3.5 28.5 - - - -
553E THR* 3.6 17.9 + - - -
559E VAL* 4.0 9.6 - - - -
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Residues in contact with ALA 502 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431E LEU* 3.8 25.6 - - + -
470E GLN* 4.2 1.6 - - - +
494E VAL* 4.0 16.8 - - + -
498E GLU 2.8 17.9 + - - +
499E PHE 3.8 3.6 - - - +
501E CYS* 1.3 77.2 - - - +
503E LEU* 1.3 61.6 + - - +
505E TYR 3.3 0.3 + - - -
506E PHE* 2.9 39.6 + - + +
529E GLU* 3.2 14.7 + - - +
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Residues in contact with LEU 503 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413E VAL* 3.8 21.5 - - + -
415E CYS* 3.7 24.6 - - - -
419E ARG* 4.0 24.2 - - - +
431E LEU* 3.6 13.2 - - + +
499E PHE* 2.8 45.7 + - + +
500E ALA* 3.6 5.8 - - - +
502E ALA* 1.3 73.1 - - - +
504E LEU* 1.3 66.8 + - - +
507E THR* 2.9 31.0 + - - -
556E GLU* 3.7 18.2 - - + +
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Residues in contact with LEU 504 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500E ALA 3.0 15.5 + - - +
501E CYS* 3.6 6.1 - - - +
503E LEU* 1.3 78.5 - - - +
505E TYR* 1.3 62.6 + - - +
507E THR* 3.8 1.2 - - - -
508E GLY 3.1 19.8 + - - +
512E PHE* 4.1 14.4 - - + -
513E ASN* 3.5 8.0 - - - +
516E MET* 4.0 9.2 - - + -
527E LEU* 4.0 22.4 - - + -
556E GLU* 3.5 13.0 + - + +
559E VAL* 3.7 37.0 - - + -
560E PHE* 3.8 22.7 - - + -
573E ARG* 3.4 24.3 + - - +
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Residues in contact with TYR 505 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472E LYS* 5.4 2.4 + - - -
501E CYS 3.0 16.5 + - - +
502E ALA 3.8 1.8 - - - +
503E LEU 3.3 0.2 - - - -
504E LEU* 1.3 75.6 - - - +
506E PHE* 1.3 91.5 + + - +
508E GLY* 3.2 6.2 + - - -
513E ASN* 2.9 41.8 + - - +
517E ARG* 4.3 10.1 - - - -
528E SER* 4.9 4.0 - - - +
529E GLU* 3.6 46.4 - - + +
5F 8OG 2.6 35.6 + - - -
6F G 3.5 4.5 + - - -
6G C 3.5 32.9 + - + +
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Residues in contact with PHE 506 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415E CYS* 3.3 18.6 - - + +
416E GLY* 2.8 22.5 + - - -
429E ASP* 4.2 20.5 - - + +
431E LEU* 4.4 5.6 - - + -
470E GLN* 4.0 14.6 - - - -
472E LYS* 4.2 10.5 - - + -
492E ILE* 3.8 50.5 - - + -
502E ALA* 2.9 36.8 + - + +
505E TYR* 1.3 100.2 - + - +
507E THR* 1.3 59.6 + - - +
529E GLU* 4.4 7.0 - - + -
6G C 3.7 22.2 - - + -
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Residues in contact with THR 507 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415E CYS* 3.6 7.1 - - - +
416E GLY* 3.5 9.9 - - - +
419E ARG* 2.7 48.9 + - + +
420E ARG* 2.7 52.5 + - + -
503E LEU 2.9 18.8 + - - -
504E LEU 3.8 2.5 - - - -
506E PHE* 1.3 80.2 - - - +
508E GLY* 1.3 58.3 + - - +
570E PRO* 4.2 4.5 - - + -
573E ARG* 3.9 11.2 - - - +
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Residues in contact with GLY 508 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420E ARG* 3.7 2.9 - - - -
504E LEU 3.1 9.5 + - - +
505E TYR 3.2 6.7 + - - -
507E THR* 1.3 82.4 - - - +
509E SER* 1.3 70.7 + - - -
512E PHE* 3.4 19.6 - - - -
513E ASN* 3.6 11.2 - - - -
573E ARG* 3.4 18.2 - - - +
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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