Contacts of the helix formed by residues 498 - 508 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466E GLU* 5.2 1.4 - - - +
469I GLN* 4.4 13.4 + - - +
470I GLN* 2.6 37.3 - - - +
494I VAL* 4.7 2.0 - - + -
495I PRO* 3.0 29.1 + - + +
497I SER* 1.3 86.6 + - - +
499I PHE* 1.3 66.7 + - - +
500I ALA 3.2 2.7 - - - -
501I CYS* 3.0 7.8 + - - +
502I ALA* 2.9 22.6 + - - +
530I HIS* 2.8 47.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 499 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411I LEU* 4.2 19.3 - - + -
413I VAL* 4.4 18.4 - - + -
431I LEU* 3.9 27.8 - - + -
433I THR* 3.6 28.0 - - + -
494I VAL* 4.3 6.5 - - + -
495I PRO 3.5 5.8 + - - +
496I TYR* 3.1 41.2 + + + +
497I SER 3.4 0.4 - - - -
498I GLU* 1.3 76.9 - - - +
500I ALA* 1.3 57.5 + - - +
502I ALA* 4.4 0.4 - - - -
503I LEU* 2.9 63.9 + - + +
554I PRO 5.9 1.8 - - - +
605I ACT 4.0 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 500 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496I TYR 4.8 0.2 + - - -
497I SER 5.0 0.8 + - - +
498I GLU 3.2 0.6 - - - -
499I PHE* 1.3 81.5 - - - +
501I CYS* 1.3 63.0 + - - +
503I LEU* 3.5 9.8 + - - +
504I LEU* 3.2 22.7 + - - +
553I THR* 3.0 34.5 + - - +
554I PRO 4.0 4.3 + - - +
555I THR* 3.6 26.7 - - - +
556I GLU* 3.8 9.6 - - - +
559I VAL* 4.8 2.7 - - + -
605I ACT 4.6 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 501 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498I GLU* 3.0 5.1 + - - +
500I ALA* 1.3 79.5 - - - +
502I ALA* 1.3 58.6 + - - +
504I LEU* 3.3 7.7 - - - +
505I TYR* 3.0 28.9 + - - +
527I LEU* 4.3 6.9 - - + +
528I SER 3.8 7.8 - - - +
529I GLU* 3.6 4.0 - - - +
530I HIS 3.7 7.6 - - - +
531I ALA* 3.6 38.8 - - - +
532I LEU 3.7 8.7 - - - -
553I THR* 3.5 23.1 - - - -
559I VAL* 3.9 17.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431I LEU* 3.8 23.1 - - + -
470I GLN* 4.2 8.3 - - - +
494I VAL* 4.3 7.4 - - + -
498I GLU 2.9 15.8 + - - +
499I PHE 3.8 4.7 - - - +
501I CYS* 1.3 74.4 - - - +
503I LEU* 1.3 65.8 + - - +
504I LEU 3.1 1.1 - - - -
505I TYR* 4.5 1.1 - - - +
506I PHE* 2.9 40.1 + - + +
529I GLU 3.3 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413I VAL* 3.3 34.8 - - + -
415I CYS* 4.0 8.0 - - - -
419I ARG* 4.0 25.6 - - - +
431I LEU* 3.6 9.1 - - + +
499I PHE* 2.9 61.8 + - + +
500I ALA* 3.6 4.3 - - - +
502I ALA* 1.3 77.0 - - - +
504I LEU* 1.3 59.2 + - - +
507I THR* 2.4 36.6 + - - -
556I GLU* 3.5 13.0 - - + +
605I ACT 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 504 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500I ALA 3.2 8.7 + - - +
501I CYS* 3.3 10.5 - - - +
502I ALA 3.1 0.2 - - - -
503I LEU* 1.3 78.6 - - - +
505I TYR* 1.3 65.8 + - - +
507I THR* 3.2 2.1 + - - -
508I GLY 3.0 20.3 + - - +
512I PHE* 4.9 3.5 - - + -
513I ASN* 3.5 9.8 - - - +
516I MET* 4.2 13.9 - - + -
527I LEU* 4.6 14.1 - - + -
556I GLU* 3.4 10.8 - - + +
559I VAL* 3.5 43.5 - - + -
560I PHE* 4.0 22.7 - - + -
573I ARG* 3.5 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 505 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472I LYS* 5.7 1.3 - - - -
501I CYS 3.0 14.6 + - - +
502I ALA 3.9 2.0 - - - +
504I LEU* 1.3 76.5 - - - +
506I PHE* 1.3 91.8 + + - +
508I GLY 3.1 6.1 + - - -
513I ASN* 2.9 32.6 + - - +
517I ARG* 4.0 7.0 - - - -
528I SER* 4.9 3.6 - - - +
529I GLU* 3.6 39.5 - - + -
601I 1RY 3.3 44.2 - - + +
5J G 2.7 37.9 + + - -
6J G 4.1 1.2 + - - -
6K C 3.5 19.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 506 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415I CYS* 3.4 19.9 - - + +
416I GLY* 2.8 20.6 + - - -
429I ASP* 4.7 11.2 - - + +
431I LEU* 4.8 6.3 - - + -
470I GLN* 4.1 16.2 - - - -
472I LYS* 4.5 8.5 - - + -
492I ILE* 4.1 48.2 - - + -
502I ALA* 2.9 37.4 + - + +
505I TYR* 1.3 104.5 - + - +
507I THR* 1.3 60.7 + - - +
529I GLU* 4.5 4.0 - - + -
601I 1RY 4.0 19.7 - - - +
6K C 3.7 21.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 507 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415I CYS* 4.0 3.3 - - - +
416I GLY* 3.6 13.3 - - - +
419I ARG* 2.6 39.3 + - + +
420I ARG* 2.7 52.2 + - + -
503I LEU 2.4 26.0 + - - -
504I LEU 3.2 3.3 + - - -
506I PHE* 1.3 78.2 - - - +
508I GLY* 1.3 56.7 + - - +
570I PRO* 4.3 10.1 - - + -
573I ARG* 4.1 13.0 - - - +
601I 1RY 4.5 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 508 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420I ARG* 4.0 2.0 - - - -
504I LEU 3.0 10.3 + - - +
505I TYR 3.1 7.7 + - - -
507I THR* 1.3 81.5 - - - +
509I SER* 1.3 70.0 + - - -
512I PHE* 4.0 4.0 - - - +
513I ASN* 3.5 14.9 - - - +
573I ARG* 3.4 29.7 - - - +
601I 1RY 4.3 5.6 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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