Contacts of the helix formed by residues 548 - 564 (chain D) in PDB entry 3T6A
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 ASP 548 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D ASN* 1.3 75.0 - - - +
549D PRO* 1.3 77.4 - - + +
550D LYS* 3.3 21.2 + - - +
551D VAL* 3.0 47.1 + - - +
552D ILE* 3.2 11.1 + - - +
629D LYS* 4.1 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ASP* 1.3 91.8 - - + +
550D LYS* 1.3 55.8 + - - +
552D ILE* 3.4 5.6 + - + +
553D ALA* 2.9 28.1 + - - +
629D LYS* 4.2 16.8 - - + +
632D GLN* 3.6 35.7 - - + +
633D VAL* 3.7 32.6 - - + +
636D GLU* 3.9 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 550 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ASP* 3.1 16.0 + - - +
549D PRO* 1.3 78.4 - - - +
551D VAL* 1.3 58.5 + - + +
553D ALA* 3.1 4.1 + - - +
554D GLN* 2.8 41.7 + - + +
636D GLU* 2.9 40.2 + - - +
640D SER* 3.2 21.2 + - - -
641D MET* 4.0 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 551 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547D ASN* 4.2 20.0 - - + +
548D ASP* 3.0 27.9 + - - +
550D LYS* 1.3 73.1 - - + +
552D ILE* 1.3 66.4 + - - +
554D GLN* 3.3 17.9 + - - +
555D HIS* 2.8 52.0 + - + -
768D PHE* 5.3 0.4 - - + -
771D ASP* 6.1 0.9 - - + -
774D MET* 5.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 552 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D PHE* 3.8 35.0 - - + +
547D ASN* 3.7 22.2 - - + +
548D ASP 3.2 8.1 + - - +
549D PRO 3.6 5.4 - - - +
551D VAL* 1.3 75.1 - - - +
553D ALA* 1.3 63.2 + - - +
555D HIS* 3.2 8.1 + - - +
556D VAL* 3.0 26.9 + - + +
629D LYS* 4.1 7.9 - - + -
633D VAL* 4.0 28.7 - - + -
774D MET* 4.1 23.3 - - + -
836D UNX 4.4 1.1 - - - -
837D UNX 3.9 21.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 553 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549D PRO 2.9 17.4 + - - +
550D LYS* 3.5 5.2 - - - +
552D ILE* 1.3 78.9 - - - +
554D GLN* 1.3 56.2 + - - +
556D VAL* 4.5 1.1 - - - -
557D LEU* 2.9 30.1 + - - +
633D VAL* 4.2 4.7 - - + +
636D GLU* 3.6 23.8 - - + -
637D LEU* 3.9 20.9 - - + +
641D MET* 3.6 19.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 554 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550D LYS* 2.8 29.3 + - - +
551D VAL* 3.7 21.6 + - - +
552D ILE 3.3 0.2 - - - -
553D ALA* 1.3 73.4 - - - +
555D HIS* 1.3 59.2 + - - +
557D LEU* 3.5 1.9 + - - +
558D SER* 3.0 29.5 + - - -
641D MET* 3.6 25.8 - - + +
764D ILE 4.7 7.7 + - - -
765D LEU* 4.0 12.1 - - + +
768D PHE* 3.6 45.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 555 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551D VAL* 2.8 38.1 + - + -
552D ILE 3.2 6.3 + - - +
554D GLN* 1.3 77.3 - - - +
556D VAL* 1.3 65.1 + - - +
558D SER* 3.3 4.6 + - - -
559D MET* 3.0 24.8 + - - +
768D PHE* 3.4 30.5 - + - -
769D GLN 4.8 1.3 - - - -
770D PRO* 4.2 1.1 - - + -
771D ASP* 2.9 33.7 + - + -
774D MET* 3.2 38.0 - - + +
775D ASN* 3.9 23.8 + - + -
778D CYS* 3.8 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 556 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D ILE* 3.0 26.3 + - + +
553D ALA* 3.9 3.6 - - - +
555D HIS* 1.3 72.5 - - - +
557D LEU* 1.3 66.5 + - - +
559D MET* 3.4 3.7 + - - +
560D ASP* 2.9 29.6 + - - +
601D ARG* 5.0 2.7 - - - +
605D MET* 4.7 8.7 - - + -
633D VAL* 5.7 1.6 - - + -
637D LEU* 4.0 15.0 - - + -
646D SER* 3.2 38.4 - - - +
650D LEU* 6.1 1.3 - - + -
778D CYS* 3.9 19.5 - - - -
837D UNX 4.6 2.2 - - - -
838D UNX 4.3 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553D ALA 2.9 18.2 + - - +
554D GLN 3.6 3.8 - - - +
556D VAL* 1.3 78.7 - - - +
558D SER* 1.3 61.9 + - - +
560D ASP* 3.7 0.7 - - - +
561D CYS* 3.0 29.7 + - - -
637D LEU* 4.7 0.2 - - - +
641D MET* 3.8 37.9 - - + +
643D ASP* 3.5 17.0 + - + +
706D SER* 3.8 18.6 - - - +
707D VAL* 3.7 26.0 - - + -
761D ALA* 4.9 2.7 - - - +
764D ILE* 3.9 9.0 - - + -
765D LEU* 3.8 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 558 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554D GLN 3.0 18.4 + - - -
555D HIS* 3.7 4.0 - - - -
556D VAL 3.3 0.2 - - - -
557D LEU* 1.3 77.8 - - - +
559D MET* 1.3 63.5 + - - +
561D CYS* 3.3 4.6 + - - +
562D ARG* 3.2 33.4 + - - +
567D LEU* 5.8 1.5 - - - +
765D LEU* 4.1 16.1 - - - +
768D PHE* 4.1 20.8 - - - -
775D ASN* 4.9 9.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 559 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515D PHE* 6.3 1.6 - - + -
555D HIS 3.0 17.1 + - - +
556D VAL 4.0 0.9 - - - +
558D SER* 1.3 72.9 - - - +
560D ASP* 1.3 67.1 + - - +
562D ARG* 3.0 35.8 + - + +
563D VAL* 2.9 37.0 + - + +
601D ARG* 3.4 17.0 - - - +
775D ASN* 5.0 9.1 - - - +
778D CYS* 3.2 29.2 - - + +
779D LYS* 3.1 40.6 - - + +
780D THR 4.7 2.2 - - - +
781D GLU* 6.3 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 560 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556D VAL 2.9 16.5 + - - +
557D LEU 3.7 1.8 - - - +
559D MET* 1.3 76.2 - - - +
561D CYS* 1.3 57.8 + - - +
562D ARG 3.2 0.2 + - - -
563D VAL* 3.3 2.2 + - - +
564D ALA* 2.9 34.3 + - - +
601D ARG* 2.8 33.8 + - - +
643D ASP* 2.4 31.1 - - - +
645D TYR* 3.6 17.3 - - + -
646D SER* 2.7 24.0 + - - -
707D VAL* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 561 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557D LEU* 3.0 36.7 + - - +
558D SER* 3.8 5.6 - - - +
559D MET 3.2 0.2 - - - -
560D ASP* 1.3 76.5 - - - +
562D ARG* 1.3 57.1 + - - +
565D ARG 3.2 3.6 + - - -
566D ILE* 2.7 46.5 + - + -
567D LEU* 3.1 30.3 + - + -
706D SER 4.8 0.4 - - - -
707D VAL* 4.1 9.6 - - - -
761D ALA* 3.8 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 562 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558D SER* 3.2 22.4 + - - +
559D MET* 3.0 32.9 + - + +
561D CYS* 1.3 77.4 - - - +
563D VAL* 1.3 67.0 + - - +
565D ARG* 3.2 15.9 + - - +
567D LEU* 3.8 21.7 - - + +
568D GLY* 4.7 8.7 - - - +
573D MET* 5.8 2.4 - - - +
775D ASN* 3.8 25.3 + - - +
779D LYS* 4.3 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 563 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515D PHE* 4.4 24.9 - - + -
559D MET* 2.9 38.0 + - + +
560D ASP* 4.0 3.1 - - - +
562D ARG* 1.3 76.4 - - - +
564D ALA* 1.3 58.8 + - - +
565D ARG* 3.1 8.5 + - - +
594D LEU* 3.5 17.0 - - - +
597D ASP* 4.9 10.5 - - + +
598D ILE* 4.7 14.6 - - + -
601D ARG* 4.1 33.2 - - - +
645D TYR* 5.6 0.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 564 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560D ASP 2.9 17.6 + - - +
563D VAL* 1.3 76.2 - - + +
565D ARG* 1.3 70.6 + - - +
566D ILE* 3.4 21.0 + - + +
582D GLY* 3.3 20.5 + - - -
583D LEU* 3.9 11.6 + - + -
594D LEU* 4.3 4.0 - - - +
598D ILE* 4.8 13.0 - - + -
645D TYR* 6.5 1.6 - - + -
707D VAL* 5.1 3.6 - - + -
710D LEU* 4.8 13.7 - - + -
----------------------------------------------------------
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