Contacts of the strand formed by residues 606 - 624 (chain A) in PDB entry 1QWN
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 THR 606 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599A HIS 3.6 0.3 - - - +
600A HIS* 3.7 2.3 + - - -
601A ASP* 2.8 28.2 + - - +
604A THR* 2.9 30.4 + - - +
605A LYS* 1.3 84.1 - - - +
607A ILE* 1.3 66.3 + - - +
608A HIS* 3.3 14.8 - - - -
653A ARG* 3.9 23.5 + - - +
744A VAL* 5.0 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 607 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A TRP* 3.6 15.2 - - + -
599A HIS 3.3 13.5 - - - +
600A HIS* 3.9 23.3 - - + +
606A THR* 1.3 75.5 - - - +
608A HIS* 1.3 62.9 + - - +
744A VAL* 3.5 21.4 + - - +
759A GLY* 3.9 27.0 - - - +
760A LEU 3.6 29.2 - - - +
761A PRO* 4.4 8.7 - - + -
762A SER 5.1 1.6 - - - +
764A VAL* 4.7 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 608 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598A TRP* 3.6 6.3 - - - -
599A HIS* 2.9 34.2 + - + +
601A ASP* 2.8 36.6 + - + +
604A THR* 4.3 0.6 + - - -
606A THR* 3.3 22.7 - - - -
607A ILE* 1.3 75.2 - - - +
609A PRO* 1.3 81.1 + - + +
610A GLN* 4.1 23.5 + - + -
653A ARG* 3.6 24.3 + - - +
657A THR* 6.0 1.3 - - - -
659A LEU* 5.9 1.0 - - - +
744A VAL* 4.2 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 609 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596A TRP* 4.0 18.0 - - + -
597A SER 3.3 9.2 - - - +
598A TRP* 3.6 37.5 - - + +
608A HIS* 1.3 94.0 + - + +
610A GLN* 1.3 68.3 + - - +
651A LEU* 3.6 23.1 - - + -
659A LEU* 3.6 15.5 - - + +
744A VAL* 3.8 11.9 - - + -
746A LEU* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 610 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL 3.7 0.5 - - - +
596A TRP* 3.4 5.0 - - - -
597A SER* 2.7 33.1 + - - +
599A HIS* 3.2 34.1 - - + +
608A HIS* 4.1 22.5 + - + +
609A PRO* 1.3 83.1 - - - +
611A GLY* 1.3 63.5 + - - +
659A LEU* 3.9 12.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 611 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595A VAL 3.4 7.2 - - - -
596A TRP* 3.6 20.8 - - - -
610A GLN* 1.3 78.0 + - - +
612A SER* 1.3 64.1 + - - -
613A THR* 3.8 8.8 + - - +
659A LEU* 4.9 3.8 - - - +
660A PRO 4.3 3.8 + - - +
661A LEU* 3.9 14.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 612 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594A PRO* 5.5 0.2 - - - +
595A VAL* 3.0 27.0 + - - +
611A GLY* 1.3 74.6 - - - -
613A THR* 1.3 59.0 + - - +
614A THR* 3.3 7.5 + - - -
615A LYS* 3.0 48.5 + - - +
616A TYR* 4.3 3.5 - - - -
661A LEU* 3.9 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 613 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611A GLY 4.3 4.7 - - - +
612A SER* 1.3 73.9 + - - +
614A THR* 1.3 70.5 + - - +
616A TYR* 3.1 18.7 + - - -
660A PRO* 3.6 33.9 - - + +
661A LEU 4.0 2.2 - - - -
662A GLY* 3.7 21.4 - - - +
663A GLN* 4.5 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 614 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A THR* 5.4 0.2 - - - +
574A SER* 3.5 26.4 - - - +
612A SER* 3.4 5.6 + - - -
613A THR* 1.3 94.6 + - - +
615A LYS* 1.3 66.7 + - - +
616A TYR* 3.8 9.4 - - - -
663A GLN* 5.9 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 615 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ASP* 3.4 31.5 + - - -
540A ARG 5.0 3.2 + - - -
542A THR* 3.0 32.3 + - + +
572A TYR* 3.8 28.8 - - + -
573A VAL 3.5 8.3 - - - +
595A VAL* 3.7 26.8 + - + +
612A SER* 3.0 27.1 + - - +
614A THR* 1.3 84.4 - - - +
616A TYR* 1.3 72.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 616 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A TYR* 3.2 6.1 - - - +
573A VAL* 2.9 42.4 + - + +
574A SER 4.3 1.6 - - - -
575A SER* 3.6 23.1 - - - +
576A PRO* 3.7 18.6 - - + -
592A VAL* 4.0 13.2 - - + -
593A SER 3.8 8.5 - - - +
594A PRO* 4.6 5.2 - - + -
595A VAL* 3.7 8.7 - - - +
612A SER 4.3 6.1 - - - -
613A THR 3.1 20.3 + - - -
614A THR* 3.8 17.7 - - - -
615A LYS* 1.3 80.1 - - - +
617A ARG* 1.3 59.4 + - - +
618A ILE 4.1 0.2 - - - -
661A LEU* 2.7 30.2 + - + -
663A GLN* 3.2 14.2 + - - +
664A TYR* 3.7 34.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 617 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ARG* 5.3 0.4 - - - +
570A ASP* 3.2 30.5 + - - +
571A PHE 3.4 4.5 - - - +
572A TYR* 3.6 28.5 - - + -
573A VAL* 4.8 0.2 - - - -
591A GLN 3.7 0.5 - - - +
592A VAL* 3.1 8.1 - - - +
593A SER* 2.8 51.9 + - - +
594A PRO 3.8 12.5 + - - +
595A VAL* 3.8 9.2 - - + +
596A TRP 5.9 0.2 - - - +
616A TYR* 1.3 72.8 - - - +
618A ILE* 1.3 60.0 + - - +
619A ILE* 3.7 21.9 - - + +
748A THR* 6.2 0.4 - - - +
753A GLU* 2.9 35.5 + - - -
770A ARG* 4.6 4.9 - - - +
777A ARG* 5.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 618 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
569A VAL 3.8 0.3 - - - +
570A ASP* 3.1 4.5 - - - -
571A PHE* 2.9 46.7 + - + +
573A VAL* 3.8 25.1 - - + -
578A VAL* 3.5 42.0 - - + +
580A VAL* 3.9 20.0 - - + -
590A ALA* 3.9 15.0 - - + -
591A GLN 3.4 7.9 - - - +
592A VAL* 4.0 13.2 - - + -
616A TYR 4.0 0.8 + - - -
617A ARG* 1.3 73.5 - - - +
619A ILE* 1.3 64.0 + - - +
620A PHE* 5.0 2.8 - - + -
634A LEU* 4.2 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 619 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568A LEU* 3.9 32.8 - - + -
569A VAL 3.2 10.1 - - - +
570A ASP* 3.8 6.1 - - + -
590A ALA* 3.2 5.8 - - - +
591A GLN* 2.8 54.3 + - + +
593A SER* 3.7 23.6 - - - +
617A ARG* 3.7 24.7 - - - +
618A ILE* 1.3 80.1 - - - +
620A PHE* 1.3 64.1 + - - +
752A LEU* 3.8 10.0 - - + +
753A GLU* 3.6 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 620 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A VAL* 4.3 2.0 - - + -
557A MET* 4.0 13.5 - - + -
568A LEU* 3.3 6.2 - - - -
569A VAL* 2.9 56.2 + - + +
571A PHE* 3.9 21.3 - + - -
580A VAL* 3.8 22.0 - - + -
588A VAL* 4.0 12.8 - - + -
589A GLU 3.5 19.1 - - - +
590A ALA* 4.2 6.1 - - + -
618A ILE* 5.0 2.7 - - + -
619A ILE* 1.3 80.1 - - - +
621A LYS* 1.3 74.1 + - - +
622A ALA* 4.4 1.1 - - + -
632A TYR* 3.7 41.5 - + + -
634A LEU* 4.2 10.1 - - + -
752A LEU* 4.3 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 621 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566A GLU* 3.7 50.5 + - + +
567A GLN 3.7 7.9 - - - +
568A LEU* 3.8 17.6 - - + +
588A VAL* 4.0 11.8 - - + +
589A GLU 4.4 4.4 + - - +
620A PHE* 1.3 82.8 - - - +
622A ALA* 1.3 61.1 + - - +
623A ARG* 4.1 1.8 + - + +
632A TYR* 4.1 4.2 + - - -
752A LEU* 5.0 2.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 622 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A MET* 4.0 17.7 - - + -
565A ARG 3.7 0.9 - - - +
566A GLU* 3.1 5.9 - - - +
567A GLN 2.9 35.7 + - - +
569A VAL* 4.1 10.5 - - + -
620A PHE* 3.5 3.5 + - + -
621A LYS* 1.3 75.2 - - - +
623A ARG* 1.3 60.1 + - - +
624A VAL* 4.1 3.6 - - + -
632A TYR* 3.6 19.1 - - + -
929A LEU* 3.9 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 623 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A TRP* 3.4 57.1 - - + +
565A ARG 3.5 5.4 - - - +
566A GLU* 3.8 30.7 - - + +
621A LYS* 4.1 1.7 + - + +
622A ALA* 1.3 72.5 - - - +
624A VAL* 1.3 62.2 + - - +
625A PRO* 4.5 1.6 - - - +
630A ALA* 3.5 16.5 - - - +
632A TYR* 3.0 14.3 + - - +
945A GLN* 5.5 1.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 624 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A MET* 3.7 36.3 - - + +
559A ASN* 3.5 21.4 + - + +
564A TRP* 3.4 6.7 - - - -
565A ARG 2.9 31.5 + - - +
622A ALA* 4.2 1.3 - - + -
623A ARG* 1.3 83.4 - - - +
625A PRO* 1.4 79.7 - - + +
628A GLY 3.4 23.6 - - - +
629A LEU* 4.0 2.7 - - - -
630A ALA* 4.2 4.7 - - + -
929A LEU* 3.9 20.2 - - + -
----------------------------------------------------------
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