Contacts of the strand formed by residues 609 - 627 (chain A) in PDB entry 4DXT
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 GLY 609 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564A SER* 2.9 15.3 - - - -
604A PHE* 3.4 21.6 - - - -
608A GLN* 1.3 76.8 - - - +
610A PHE* 1.3 69.8 + - - +
693A ARG* 3.6 2.8 - - - +
694A ILE* 2.8 28.6 + - - +
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Residues in contact with PHE 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A ARG* 3.5 31.6 - - - -
563A CYS* 3.5 17.3 - - - -
564A SER* 2.7 57.4 + - - -
602A TRP* 3.6 7.5 - - - -
604A PHE* 4.7 2.4 - - - -
609A GLY* 1.3 81.5 - - - +
611A ALA* 1.3 64.1 - - - +
691A GLU* 3.5 22.7 - - + +
692A LEU 2.9 13.5 - - - +
693A ARG* 4.0 9.2 - - + -
694A ILE* 5.4 1.3 - - - -
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Residues in contact with ALA 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A VAL* 4.6 4.3 - - + -
562A ARG 4.0 1.3 - - - -
563A CYS* 3.7 18.8 - - - -
588A PRO* 5.3 0.4 - - + -
591A ILE* 4.0 27.1 - - + -
602A TRP* 4.0 13.0 - - + -
610A PHE* 1.3 76.1 - - - +
612A VAL* 1.3 63.9 + - - +
613A VAL* 4.1 2.9 + - + +
690A VAL 4.1 0.3 - - - +
691A GLU* 3.2 2.4 - - - -
692A LEU* 2.7 42.7 + - + +
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Residues in contact with VAL 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A VAL* 3.4 8.1 - - - +
559A ILE* 3.0 41.9 + - + -
562A ARG* 3.1 50.2 + - + +
563A CYS* 3.8 0.4 - - - -
610A PHE* 5.0 1.1 - - + -
611A ALA* 1.3 77.2 - - - +
613A VAL* 1.3 62.9 + - - +
651A PHE* 5.1 1.6 - - + -
656A GLN* 3.9 10.1 - - - +
689A VAL* 3.6 28.5 - - + -
690A VAL 3.4 5.4 - - - +
691A GLU* 3.8 20.6 - - + +
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Residues in contact with VAL 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ALA* 4.1 8.1 - - + -
556A ALA* 4.6 0.2 - - + -
557A SER 3.6 10.1 - - - +
558A VAL* 5.1 2.5 - - + -
591A ILE* 4.6 9.4 - - + -
592A LEU* 4.0 35.4 - - + -
611A ALA* 4.6 4.5 - - + +
612A VAL* 1.3 81.0 - - - +
614A ARG* 1.3 71.2 + - - +
615A LEU* 3.7 19.1 + - + +
689A VAL* 3.3 6.6 - - - -
690A VAL* 2.7 39.9 + - + +
709A PHE* 4.2 23.3 - - + -
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Residues in contact with ARG 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A GLY 4.6 0.3 - - - +
556A ALA* 3.3 2.3 - - - +
557A SER* 2.8 49.3 + - - +
559A ILE* 4.2 27.6 - - + +
612A VAL 4.2 0.6 + - - -
613A VAL* 1.3 71.5 - - - +
615A LEU* 1.3 73.3 + - - +
654A ASP* 5.5 8.7 - - - +
688A GLN* 3.4 22.7 - - + +
689A VAL* 4.2 19.2 - - + +
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Residues in contact with LEU 615 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A TYR* 3.3 17.7 - - + +
555A GLY 4.6 1.6 - - - +
556A ALA* 4.2 0.9 - - - -
613A VAL* 4.0 18.4 - - + +
614A ARG* 1.3 79.5 - - - +
616A SER* 1.3 64.4 + - - +
617A ALA 3.4 12.6 - - - +
619A ILE* 3.7 36.1 - - + -
621A PRO* 5.5 0.7 - - + -
687A TYR 4.0 11.9 - - - +
688A GLN* 2.9 33.3 + - - +
690A VAL* 4.2 16.8 - - + -
711A VAL* 3.9 34.5 - - + -
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Residues in contact with SER 616 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ASP 4.6 2.1 + - - -
549A TYR* 2.8 38.4 + - - -
551A LEU 5.1 0.2 - - - -
554A GLY* 3.2 29.9 + - - -
555A GLY* 3.8 18.2 - - - -
556A ALA* 3.8 3.3 - - - +
615A LEU* 1.3 71.3 - - - +
617A ALA* 1.3 62.9 + - - +
688A GLN* 3.9 5.2 + - - -
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Residues in contact with ALA 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A TYR* 4.2 20.7 - - + -
615A LEU* 3.2 19.7 - - - +
616A SER* 1.3 81.9 + - - +
618A ARG* 1.3 69.2 + - - +
619A ILE* 3.5 8.1 + - + +
687A TYR 4.0 1.0 - - - +
688A GLN* 3.7 12.8 - - - +
715A PRO* 5.2 5.6 - - + -
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Residues in contact with ARG 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617A ALA* 1.3 74.3 - - - +
619A ILE* 1.3 66.0 + - - +
652A ASP* 3.1 37.5 + - - +
686A THR* 2.6 50.8 + - + +
687A TYR* 3.4 9.1 - - - +
688A GLN* 3.6 37.2 + - - +
715A PRO* 4.0 10.7 - - - +
716A ALA* 4.3 5.7 + - - +
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Residues in contact with ILE 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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549A TYR* 3.6 52.5 - - + -
615A LEU* 3.7 27.6 - - + -
617A ALA* 3.6 10.5 - - + +
618A ARG* 1.3 80.8 - - - +
620A ARG* 1.3 64.7 + - - +
621A PRO* 3.3 8.5 - - + +
686A THR* 3.9 7.9 - - - -
687A TYR 2.8 32.3 + - - +
711A VAL* 4.0 13.7 - - + -
712A HIS 4.0 2.0 - - - +
713A GLY* 3.9 16.2 - - - +
714A GLU 3.3 15.0 - - - +
715A PRO* 4.1 4.5 - - + -
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Residues in contact with ARG 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619A ILE* 1.3 72.6 - - - +
621A PRO* 1.3 66.3 - - + +
622A THR* 3.6 9.6 + - - +
682A PRO* 2.7 49.3 + - + +
683A THR 2.6 17.9 + - - +
684A MET* 3.6 34.0 - - + +
685A ALA 3.5 20.0 - - - +
686A THR* 4.2 10.6 - - + +
713A GLY* 3.1 2.6 - - - -
714A GLU* 2.8 73.9 + - - +
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Residues in contact with PRO 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A ILE* 3.3 18.2 - - + +
620A ARG* 1.3 85.2 - - + +
622A THR* 1.3 60.0 + - - +
662A LEU* 4.3 11.8 - - + +
679A PHE* 3.4 28.6 - - + -
682A PRO* 3.8 17.8 - - - +
685A ALA 3.8 4.9 - - - +
687A TYR* 3.8 33.4 - - + +
690A VAL* 4.9 7.6 - - + -
711A VAL* 4.7 9.4 - - + -
712A HIS 3.6 9.4 - - - +
713A GLY* 4.1 0.4 - - - -
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Residues in contact with THR 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620A ARG* 3.9 21.3 - - - +
621A PRO* 1.3 77.6 - - - +
623A ALA* 1.3 66.8 + - - +
678A HIS* 3.5 9.5 + - - +
679A PHE* 3.0 28.9 + - - +
682A PRO* 4.6 9.9 - - + -
712A HIS* 3.0 4.9 + - - +
713A GLY* 3.2 19.3 + - - -
714A GLU* 4.2 22.9 - - + +
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Residues in contact with ALA 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546A LEU* 5.4 1.6 - - + -
622A THR* 1.3 82.7 - - - +
624A VAL* 1.3 68.2 + - - +
676A THR* 4.2 4.7 - - + -
677A PHE 3.0 14.6 - - - +
678A HIS* 3.7 24.5 - - + +
679A PHE* 3.7 7.5 - - - -
711A VAL* 3.9 0.9 - - - +
712A HIS* 3.0 46.0 + - + +
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Residues in contact with VAL 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A ALA* 1.3 78.9 - - - +
625A THR* 1.3 64.0 + - - +
626A LEU* 6.1 0.2 - - + -
646A PHE* 4.3 12.6 - - + -
648A ILE* 4.0 26.2 - - + -
665A PHE* 4.6 4.3 - - + -
676A THR* 3.4 3.5 - - - +
677A PHE* 2.7 52.5 + - + +
679A PHE* 3.8 18.4 - - + -
709A PHE* 3.8 20.6 - - + -
710A ARG 3.2 14.8 - - - +
711A VAL* 4.2 10.3 - - + -
712A HIS* 4.0 2.2 - - - -
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Residues in contact with THR 625 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A ILE* 3.5 2.9 - - + +
624A VAL* 1.3 75.2 - - - +
626A LEU* 1.3 69.1 + - - +
627A GLU* 4.7 0.9 - - + +
674A ILE* 3.5 28.9 - - + -
675A GLN 3.4 11.7 - - - +
676A THR* 2.9 18.2 + - - +
708A ARG 3.8 0.6 - - - +
709A PHE* 3.4 7.6 - - - -
710A ARG* 2.8 54.9 + - - +
712A HIS* 2.7 27.1 + - - -
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Residues in contact with LEU 626 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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624A VAL* 6.1 0.2 - - + -
625A THR* 1.3 76.9 - - - +
627A GLU* 1.3 64.1 + - - +
643A PRO* 3.9 26.7 - - + -
646A PHE* 3.6 41.7 - - + -
667A TYR* 3.6 15.8 - - + -
675A GLN 2.9 29.4 + - - +
677A PHE* 4.3 12.0 - - + -
692A LEU* 4.2 8.1 - - + -
694A ILE* 5.0 1.1 - - + -
706A ILE* 4.1 22.2 - - + -
708A ARG 3.5 13.5 - - - +
709A PHE* 4.2 19.7 - - + -
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Residues in contact with GLU 627 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A PRO 5.5 0.2 - - - +
596A VAL* 3.6 35.0 - - + +
625A THR* 5.1 0.2 - - + -
626A LEU* 1.3 80.7 - - - +
628A HIS* 1.3 65.9 + - - +
643A PRO* 5.9 1.3 - - - +
667A TYR* 4.1 3.1 - - - -
673A PRO* 3.1 13.8 - - - +
674A ILE* 3.6 27.9 - - + +
707A TYR* 3.3 18.4 + - + +
708A ARG* 3.1 38.2 + - + +
710A ARG* 2.8 31.8 + - - +
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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