Contacts of the helix formed by residues 498 - 508 (chain M) in PDB entry 4K4I
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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469M GLN* 3.2 26.8 + - - +
470M GLN* 2.8 33.1 - - - +
494M VAL* 4.1 2.5 - - + -
495M PRO* 3.1 24.1 + - + +
496M TYR 3.1 0.8 - - - -
497M SER* 1.3 88.3 + - - +
499M PHE* 1.3 62.5 + - - +
500M ALA 3.4 2.2 - - - -
501M CYS* 3.4 4.9 + - - +
502M ALA* 3.0 21.8 + - - +
529M GLU 4.0 0.9 - - - +
530M HIS* 3.0 46.9 + - - +
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Residues in contact with PHE 499 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411M LEU* 4.3 17.7 - - + -
413M VAL* 4.3 20.0 - - + -
431M LEU* 3.7 31.2 - - + -
433M THR* 3.5 34.5 - - + -
494M VAL* 4.1 7.2 - - + -
495M PRO 3.6 1.8 + - - +
496M TYR* 3.0 37.5 + + + +
497M SER 3.5 0.4 - - - -
498M GLU* 1.3 77.0 - - - +
500M ALA* 1.3 65.4 + - - +
502M ALA* 3.3 0.9 + - - +
503M LEU* 2.9 46.1 + - + +
554M PRO 5.6 6.1 - - - +
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Residues in contact with ALA 500 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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496M TYR 4.8 0.2 + - - -
498M GLU 3.4 0.6 - - - -
499M PHE* 1.3 79.6 - - - +
501M CYS* 1.3 58.1 + - - +
503M LEU* 3.3 10.5 + - - +
504M LEU* 2.9 30.5 + - - +
553M THR* 3.5 23.2 + - - +
554M PRO 3.9 4.1 + - - +
555M THR* 3.3 39.7 - - - +
556M GLU* 3.3 8.9 - - - +
559M VAL* 4.7 2.5 - - + -
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Residues in contact with CYS 501 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498M GLU* 3.4 4.3 + - - +
499M PHE 3.3 0.4 - - - -
500M ALA* 1.3 79.2 - - - +
502M ALA* 1.3 57.9 + - - +
504M LEU* 3.4 7.3 + - - +
505M TYR* 3.0 28.4 + - - +
527M LEU* 4.1 8.9 - - + +
528M SER 3.7 14.1 - - - +
529M GLU* 3.6 3.6 - - - +
530M HIS 3.8 18.6 - - - +
531M ALA* 3.6 5.6 - - - -
532M LEU* 3.5 28.3 - - - -
553M THR* 3.6 19.5 + - - -
559M VAL* 4.0 15.3 - - - -
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Residues in contact with ALA 502 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431M LEU* 3.7 28.0 - - + -
470M GLN* 4.2 8.3 - - - +
494M VAL* 4.4 6.1 - - + -
498M GLU 3.0 17.6 + - - +
499M PHE 3.7 2.9 - - - +
501M CYS* 1.3 73.7 - - - +
503M LEU* 1.3 58.1 + - - +
505M TYR* 3.2 1.2 + - - +
506M PHE* 2.7 48.8 + - + +
529M GLU 3.3 14.3 + - - +
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Residues in contact with LEU 503 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413M VAL* 4.0 19.1 - - + -
415M CYS* 3.9 17.3 - - - -
419M ARG* 3.9 31.9 - - - +
431M LEU* 3.5 18.6 - - + +
499M PHE* 2.9 44.9 + - + +
500M ALA* 3.3 7.9 - - - +
502M ALA* 1.3 76.9 - - - +
504M LEU* 1.3 61.9 + - - +
506M PHE* 4.5 0.2 - - - +
507M THR* 2.7 31.2 + - - -
556M GLU* 3.6 14.1 - - + +
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Residues in contact with LEU 504 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500M ALA 2.9 17.0 + - - +
501M CYS* 3.7 6.5 - - - +
502M ALA 3.1 0.2 - - - -
503M LEU* 1.3 76.0 - - - +
505M TYR* 1.3 63.4 + - - +
507M THR* 3.8 1.6 - - - -
508M GLY 3.1 19.2 + - - +
512M PHE* 4.5 6.1 - - + -
513M ASN* 3.6 10.1 - - - +
516M MET* 3.7 28.5 - - + -
527M LEU* 4.3 13.9 - - + -
556M GLU* 3.5 12.1 - - + +
559M VAL* 3.6 40.4 - - + -
560M PHE* 3.8 16.6 - - + -
573M ARG* 3.7 21.5 + - - +
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Residues in contact with TYR 505 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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472M LYS* 5.7 1.6 - - - -
501M CYS 3.0 17.8 + - - +
502M ALA 3.7 2.5 - - - +
504M LEU* 1.3 76.9 - - - +
506M PHE* 1.3 93.1 + + - +
508M GLY 3.2 4.7 + - - -
513M ASN* 3.0 27.7 + - - +
517M ARG* 4.0 6.5 - - - -
528M SER* 4.6 3.4 - - - +
529M GLU* 3.5 41.2 + - + +
601M 1RY 3.2 48.7 - - + +
5N G 2.7 39.8 + + - -
6N G 4.0 1.2 + - - -
6O C 3.5 20.9 + - + -
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Residues in contact with PHE 506 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415M CYS* 3.4 21.0 - - + +
416M GLY* 2.8 22.2 + - - -
429M ASP* 4.7 11.6 - - + +
431M LEU* 4.4 5.4 - - + -
470M GLN* 4.2 16.2 - - - -
472M LYS* 4.4 9.9 - - + -
492M ILE* 4.0 48.9 - - + -
502M ALA* 2.7 39.1 + - + +
505M TYR* 1.3 103.5 - + - +
507M THR* 1.3 57.5 + - - +
529M GLU* 4.3 7.9 - - + -
601M 1RY 4.1 17.2 - - - +
6O C 3.8 20.4 - - - -
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Residues in contact with THR 507 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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415M CYS* 3.9 6.2 - - - +
416M GLY* 3.6 9.4 - - - +
419M ARG* 2.8 45.6 + - + +
420M ARG* 2.9 45.9 + - + +
503M LEU 2.7 22.6 + - - -
504M LEU 3.8 2.9 - - - -
506M PHE* 1.3 77.4 - - - +
508M GLY* 1.3 63.1 + - - +
570M PRO* 4.4 3.1 - - + -
573M ARG* 3.9 13.0 - - - +
601M 1RY 4.8 0.4 - - - -
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Residues in contact with GLY 508 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420M ARG* 3.8 1.5 - - - -
504M LEU 3.1 9.5 + - - +
505M TYR 3.2 8.0 + - - -
507M THR* 1.3 80.2 - - - +
509M SER* 1.3 70.6 + - - -
512M PHE* 3.8 7.8 - - - -
513M ASN* 3.5 12.6 - - - +
573M ARG* 3.5 29.3 - - - +
601M 1RY 4.1 4.7 - - - -
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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