Contacts of the helix formed by residues 529 - 548 (chain K) in PDB entry 6R1U
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 SER 529 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479K ILE* 5.7 1.2 - - - +
527K GLN 4.0 1.2 + - - -
528K PHE* 1.3 78.9 - - - +
530K GLU* 1.3 64.6 + - - +
531K LEU* 3.3 8.6 + - - +
532K GLU* 2.8 37.8 + - - +
533K GLY* 3.1 17.5 + - - -
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Residues in contact with GLU 530 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529K SER* 1.3 74.9 - - - +
531K LEU* 1.3 57.8 + - - +
533K GLY* 3.2 3.4 + - - -
534K GLN* 2.8 54.0 + - + +
686K PRO 5.1 2.1 - - - +
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Residues in contact with LEU 531 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469K GLN* 3.5 48.2 - - + +
473K ARG* 5.9 1.6 - - - -
475K THR* 4.7 1.3 - - + +
476K ASP 5.8 0.2 - - - +
479K ILE* 3.8 29.6 - - + -
529K SER* 3.2 8.3 + - - +
530K GLU* 1.3 76.4 - - - +
532K GLU* 1.3 60.8 + - + +
534K GLN* 2.9 21.4 + - - +
535K VAL* 2.8 48.0 + - + +
684K VAL* 4.3 4.7 - - + -
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Residues in contact with GLU 532 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479K ILE* 4.1 20.2 - - + +
482K ARG* 2.9 37.8 + - - -
483K MET* 3.2 32.1 - - - +
527K GLN 4.3 1.4 - - - +
528K PHE* 3.0 28.5 - - + +
529K SER* 2.8 44.5 + - - +
531K LEU* 1.3 76.0 - - - +
533K GLY* 1.3 63.2 + - - +
535K VAL* 3.4 3.2 + - - -
536K LEU 3.2 16.6 + - - -
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Residues in contact with GLY 533 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483K MET* 5.1 0.4 - - - -
517K TYR* 4.7 13.0 - - - -
528K PHE* 4.6 1.0 - - - +
529K SER 3.1 13.6 + - - -
530K GLU* 3.2 4.9 + - - -
532K GLU* 1.3 78.3 - - - +
534K GLN* 1.3 60.3 + - - +
536K LEU* 3.4 9.4 + - - +
537K GLN* 3.1 28.1 + - - +
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Residues in contact with GLN 534 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530K GLU* 2.8 44.5 + - + +
531K LEU* 2.9 25.6 + - - +
533K GLY* 1.3 73.9 - - - +
535K VAL* 1.3 63.9 + - - +
537K GLN* 3.2 8.8 + - + +
538K PHE 3.1 5.5 + - - -
684K VAL* 3.6 11.6 - - + +
685K PRO* 3.1 44.0 - - - +
686K PRO* 3.0 31.6 + - - +
687K SER* 5.6 1.1 - - - -
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Residues in contact with VAL 535 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467K LEU* 3.8 22.9 - - + -
475K THR* 4.3 20.0 - - + +
479K ILE* 4.4 9.4 - - + +
480K ASP* 5.0 5.6 - - - -
483K MET* 3.8 21.8 - - + -
531K LEU* 2.8 37.5 + - + +
532K GLU 3.7 5.8 - - - +
533K GLY 3.3 0.2 - - - -
534K GLN* 1.3 73.6 - - - +
536K LEU* 1.3 65.8 + - - +
538K PHE* 3.0 17.4 + - - +
539K HIS* 3.2 19.2 - - + +
684K VAL* 4.5 7.9 - - + -
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Residues in contact with LEU 536 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483K MET* 4.2 15.9 - - + +
486K HIS* 5.9 1.8 - - + -
487K PHE* 3.7 43.3 - - + +
490K LEU* 4.5 9.6 - - + -
513K ILE* 6.4 0.2 - - + -
517K TYR* 3.5 45.5 - - + +
532K GLU 3.2 10.6 + - - +
533K GLY* 3.4 10.3 - - - +
535K VAL* 1.3 79.0 - - - +
537K GLN* 1.3 63.8 + - + +
539K HIS* 3.2 7.2 + - - +
540K LEU* 3.0 34.4 + - + +
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Residues in contact with GLN 537 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514K GLU* 5.9 1.4 + - - -
533K GLY 3.1 17.1 + - - +
534K GLN* 3.2 15.5 - - + +
535K VAL 3.1 0.4 - - - -
536K LEU* 1.3 78.4 - - - +
538K PHE* 1.3 64.7 + - - +
540K LEU* 3.2 18.0 + - - +
541K SER* 2.9 23.0 + - - -
685K PRO* 3.8 16.6 - - + -
687K SER* 4.9 1.3 - - - -
688K ALA* 3.2 31.5 - - + +
691K ARG* 2.8 37.7 + - + +
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Residues in contact with PHE 538 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465K CYS* 5.1 0.7 - - - -
467K LEU* 3.6 37.0 - - + -
534K GLN 3.1 5.4 + - - +
535K VAL* 3.0 13.3 + - - +
537K GLN* 1.3 77.0 - - - +
539K HIS* 1.3 76.0 + + - +
541K SER* 3.0 16.0 + - - -
542K ASN* 3.0 19.8 + - + +
682K GLY* 4.0 9.4 - - - -
683K HIS 3.7 19.3 - - - -
684K VAL* 4.9 2.7 - - + -
685K PRO* 3.6 18.8 - - + +
695K ALA* 3.3 30.3 - - + -
696K VAL* 4.0 17.3 - - + -
8M ARG* 3.8 30.5 - - + -
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Residues in contact with HIS 539 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467K LEU* 4.6 3.6 - - - +
480K ASP* 4.9 1.0 + - - -
483K MET 4.5 4.0 - - - -
484K ASP* 3.9 35.8 + - + +
487K PHE* 3.6 53.8 - + + -
488K ASN* 5.8 0.2 - - - -
535K VAL* 3.2 35.7 + - + +
536K LEU* 3.2 9.3 + - - +
538K PHE* 1.3 91.1 - + - +
540K LEU* 1.3 66.4 + - - +
542K ASN* 3.1 16.2 + - - +
543K LEU* 3.2 9.4 + - - +
8M ARG* 4.3 28.3 + - + -
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Residues in contact with LEU 540 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487K PHE* 3.8 24.7 - - + -
513K ILE* 4.2 32.1 - - + -
514K GLU* 6.3 3.1 - - + -
536K LEU* 3.0 25.5 + - + +
537K GLN* 3.2 21.7 + - - +
539K HIS* 1.3 76.5 - - - +
541K SER* 1.3 64.3 + - - +
543K LEU* 3.1 17.1 + - - +
544K GLU* 3.2 16.9 + - - +
551K LEU* 4.1 9.5 - - + +
691K ARG* 3.3 34.1 - - - +
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Residues in contact with SER 541 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537K GLN 2.9 13.4 + - - -
538K PHE* 3.1 12.8 - - - -
540K LEU* 1.3 78.3 - - - +
542K ASN* 1.3 56.7 - - - +
544K GLU* 3.2 14.6 + - - +
545K TYR* 3.0 26.3 + - - +
691K ARG* 2.8 37.1 + - - +
692K GLY* 3.4 9.7 - - - -
695K ALA* 3.6 13.7 - - - +
714K ALA* 4.7 1.9 - - - +
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Residues in contact with ASN 542 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538K PHE* 3.0 19.7 + - + +
539K HIS* 3.4 15.1 + - - +
540K LEU 3.1 0.2 - - - -
541K SER* 1.3 76.0 - - - +
543K LEU* 1.3 62.5 + - - +
545K TYR* 3.6 17.4 + - - +
546K ALA* 3.2 16.5 + - - +
696K VAL* 4.5 13.5 - - - +
5M GLN* 3.1 30.5 + - - +
7M ALA* 3.1 17.0 + - - +
8M ARG* 2.8 35.7 + - - +
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Residues in contact with LEU 543 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487K PHE* 3.4 40.6 - - + -
491K LEU* 4.4 8.3 - - + -
509K LEU* 4.6 6.5 - - + -
513K ILE* 4.3 10.8 - - + -
539K HIS 3.2 4.7 + - - +
540K LEU* 3.1 8.9 + - + +
542K ASN* 1.3 76.1 - - - +
544K GLU* 1.3 56.9 + - - +
546K ALA* 3.2 5.3 + - + +
547K CYS* 3.0 33.8 + - - -
551K LEU* 3.9 29.6 - - + -
559K TRP* 4.3 22.0 - - + -
5M GLN* 3.4 22.0 - - - +
10M SER* 4.0 12.3 - - - +
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Residues in contact with GLU 544 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540K LEU 3.2 12.3 + - - +
541K SER* 3.2 9.3 + - - +
543K LEU* 1.3 75.1 - - - +
545K TYR* 1.3 55.8 + - - +
548K GLY* 2.7 31.4 + - - -
549K SER 3.1 23.6 + - - +
550K ASN* 3.2 14.5 + - - -
551K LEU* 2.9 33.6 + - + -
691K ARG* 2.9 51.6 + - - +
692K GLY* 5.0 1.7 + - - -
714K ALA* 4.3 4.5 - - + +
715K GLY* 4.0 17.7 - - - +
716K GLU* 4.7 2.1 + - - +
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Residues in contact with TYR 545 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438K ILE* 4.5 14.4 - - - +
541K SER 3.0 15.6 + - - +
542K ASN* 3.7 22.9 - - - +
544K GLU* 1.3 79.0 - - - +
546K ALA* 1.3 64.8 + - + +
548K GLY 3.3 4.2 + - - -
659K ILE* 3.9 14.7 - - + +
661K LYS* 6.1 1.1 - - - -
696K VAL* 6.5 0.2 - - + -
698K TYR* 4.0 18.4 + - - -
712K VAL* 3.7 33.9 - - + -
714K ALA* 3.8 16.2 - - + +
767K TYR* 2.7 39.6 + - - -
901K FAD 4.9 7.3 + - - -
4M MET* 3.9 31.7 + - + +
5M GLN* 4.7 5.2 - - + -
6M THR* 5.1 4.8 + - - -
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Residues in contact with ALA 546 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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542K ASN 3.2 5.4 + - - +
543K LEU* 3.2 10.3 + - + +
545K TYR* 1.3 82.7 - - - +
547K CYS* 1.3 60.2 + - - +
559K TRP* 6.1 0.7 - - + -
767K TYR* 3.5 2.9 - - - -
803K GLN* 3.0 20.8 + - - -
1M ALA 3.3 26.7 + - - +
2M ARG* 4.8 1.1 - - - -
4M MET* 3.5 19.1 - - + +
5M GLN* 3.6 29.4 - - + +
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Residues in contact with CYS 547 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509K LEU* 5.7 0.7 - - - -
543K LEU* 3.0 22.2 + - - +
546K ALA* 1.3 78.2 - - - +
548K GLY* 1.3 63.0 + - - +
549K SER 4.2 7.6 - - - +
551K LEU* 5.0 2.5 - - - -
554K VAL* 4.3 32.8 - - + -
559K TRP* 4.5 21.5 - - - -
657K GLY* 4.0 2.4 - - - -
767K TYR* 4.0 6.6 - - - +
769K PHE* 3.3 35.2 - - + +
803K GLN* 4.0 6.5 + - - +
1M ALA* 4.0 14.4 - - - +
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Residues in contact with GLY 548 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544K GLU 2.7 10.7 + - - -
545K TYR 3.3 6.2 + - - -
547K CYS* 1.3 79.3 - - - +
549K SER* 1.3 57.8 + - - +
657K GLY* 3.1 6.6 - - - -
658K ILE* 2.7 52.3 + - - +
659K ILE* 4.1 1.8 - - - -
715K GLY 5.5 1.1 - - - -
767K TYR* 3.7 12.8 - - - -
769K PHE* 4.3 0.2 - - - -
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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
------------------------------------------------------------
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