Contacts of the strand formed by residues 578 - 589 (chain A) in PDB entry 5C58
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 LEU 578 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572A ARG* 3.5 11.3 + - - +
573A PRO* 3.5 23.4 - - + +
575A VAL* 3.3 19.6 + - + +
576A GLU 3.1 0.8 - - - -
577A TRP* 1.3 97.7 - - + +
579A GLU* 1.3 67.8 + - - +
580A LEU* 3.9 21.1 - - + -
626A PHE* 3.5 39.5 - - + -
627A ASN 3.8 9.2 - - - +
628A VAL* 4.2 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 579 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A TYR 4.4 5.4 - - - +
118A ASP* 4.4 12.9 - - - +
119A GLU 5.2 0.2 - - - -
120A PRO* 4.9 7.6 - - - +
502A THR* 4.1 13.5 - - - +
570A ALA* 3.4 22.5 - - + +
571A VAL 3.4 15.0 - - - +
572A ARG* 4.2 30.5 + - + +
578A LEU* 1.3 77.9 - - - +
580A LEU* 1.3 69.7 + - - +
581A TYR* 4.0 2.0 + - + -
626A PHE* 3.1 24.7 - - - -
627A ASN* 3.2 34.4 + - - +
629A GLN* 5.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 580 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570A ALA* 3.2 4.0 - - - +
571A VAL* 2.9 45.4 + - + +
573A PRO* 4.1 24.0 - - + -
578A LEU* 3.9 19.3 - - + -
579A GLU* 1.3 72.1 - - - +
581A TYR* 1.3 62.8 + - - +
625A GLY 3.7 4.5 - - - +
626A PHE* 3.7 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 581 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 3.3 34.8 - - + -
121A ARG* 3.7 15.6 + - - -
122A SER* 4.3 0.9 - - - -
569A VAL 3.1 11.9 - - - +
570A ALA* 3.6 13.2 - - + -
579A GLU* 4.3 4.0 - - + -
580A LEU* 1.3 76.7 - - - +
582A THR* 1.3 69.9 + - - +
583A THR* 4.1 7.6 - - + -
623A GLU* 2.7 42.2 + - + -
624A VAL* 3.6 2.8 - - - +
625A GLY* 2.9 65.8 + - - +
626A PHE* 3.5 15.5 - - - -
627A ASN* 4.3 13.0 - - - -
643A LYS* 4.5 4.1 - - - +
644A VAL 4.5 0.2 + - - -
645A ALA* 3.5 13.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 582 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567A LEU 4.8 0.2 - - - -
568A ALA* 3.6 0.7 - - - -
569A VAL* 2.8 42.6 + - - +
581A TYR* 1.3 78.2 + - - +
583A THR* 1.3 67.7 + - - +
622A TRP* 3.9 28.9 - - + -
623A GLU 3.3 11.7 - - - +
624A VAL* 4.0 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 583 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 3.3 26.5 - - + +
121A ARG* 4.9 7.0 - - + -
566A THR* 6.5 0.2 - - - -
567A LEU 3.3 7.4 - - - -
568A ALA* 3.9 16.2 - - + -
569A VAL 5.0 0.2 - - - +
581A TYR* 4.1 8.1 - - + -
582A THR* 1.3 81.6 - - - +
584A TYR* 1.3 63.2 + - - +
621A ALA 3.7 0.7 - - - +
622A TRP* 3.7 8.7 - - - -
623A GLU* 2.9 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 584 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565A PRO* 5.1 7.4 - - + -
566A THR* 3.5 3.2 - - - +
567A LEU* 2.7 58.1 + - + +
583A THR* 1.3 75.6 - - - +
585A GLY* 1.3 61.3 + - - +
586A LYS* 3.3 40.2 - - + +
620A ARG* 3.7 30.3 + - + -
621A ALA 3.4 11.4 - - - -
622A TRP* 3.5 50.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 585 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 3.8 17.8 + - - +
565A PRO 3.3 11.7 - - - -
566A THR* 4.2 7.2 - - - -
584A TYR* 1.3 83.9 - - - +
586A LYS* 1.3 65.4 + - - +
620A ARG* 3.6 2.8 - - - -
621A ALA* 3.0 31.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 586 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 4.6 3.2 - - - -
213A THR 5.4 0.3 - - - +
508A ARG* 4.1 5.4 + - - -
563A LEU 5.6 2.0 - - - +
564A SER* 3.2 22.9 - - - +
565A PRO* 3.0 42.9 + - + +
566A THR* 4.9 2.1 + - - -
584A TYR* 3.3 28.3 - - + +
585A GLY* 1.3 78.3 - - - +
587A SER* 1.3 61.6 + - - +
618A ARG* 3.5 36.8 - - + +
619A SER 3.2 15.3 - - - +
620A ARG* 3.9 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 587 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 3.3 21.8 - - - +
213A THR 5.6 0.7 - - - -
221A THR* 3.3 18.6 - - - -
222A LEU* 3.3 13.9 - - - +
508A ARG* 4.5 11.2 - - - +
564A SER* 4.5 1.8 - - - -
586A LYS* 1.3 75.6 - - - +
588A TRP* 1.3 64.0 + - - +
589A ARG 4.3 0.4 - - - -
617A GLU 3.9 0.2 - - - +
618A ARG* 3.6 7.3 - - - +
619A SER* 2.2 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 588 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ALA 3.6 14.6 - - - +
221A THR 3.9 4.2 + - - -
486A VAL* 5.4 0.4 - - + -
508A ARG* 5.0 4.2 - - - +
510A ASP* 3.5 39.0 - - + +
511A ARG 4.4 1.3 - - - -
512A TYR* 3.4 17.9 - + + -
560A GLN* 3.2 38.1 - - + -
561A GLY 4.3 3.4 - - - -
562A LYS* 3.4 46.5 - - + +
564A SER* 4.0 8.4 + - - +
587A SER* 1.3 78.5 - - - +
589A ARG* 1.3 58.7 + - - +
590A PRO* 3.3 23.6 - - + +
616A PRO* 3.3 37.3 - - + +
617A GLU 3.4 15.5 - - - -
618A ARG* 4.7 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 589 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR* 3.7 32.1 + - - +
172A ARG* 3.4 38.4 - - - +
220A GLY* 3.6 23.8 - - - +
222A LEU* 4.5 11.6 - - + +
484A ARG* 5.2 3.5 - - - +
587A SER 4.3 0.6 - - - -
588A TRP* 1.3 72.1 - - - +
590A PRO* 1.3 85.7 + - + +
592A ALA* 4.1 2.8 - - - +
595A GLU* 3.0 26.5 + - - -
616A PRO* 4.0 2.2 - - - -
617A GLU* 2.8 86.4 + - - +
655A ILE* 3.6 12.3 - - - +
----------------------------------------------------------
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