Contacts of the strand formed by residues 556 - 563 (chain A) in PDB entry 1QHP
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 556 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ALA 5.0 0.3 - - - +
555A ALA* 1.3 74.9 - - - +
557A LEU* 1.3 66.6 + - - -
558A THR* 3.4 4.6 + - - -
574A TYR 3.7 0.2 - - - +
575A ASN* 3.8 7.0 - - - -
576A ILE* 2.8 33.4 + - - +
607A PRO* 3.9 20.1 - - - +
611A ASN* 5.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A LYS* 4.3 9.6 - - - +
317A TYR* 4.3 7.2 - - - +
556A GLY* 1.3 72.5 - - - -
558A THR* 1.3 60.4 + - - +
573A SER* 3.9 27.4 - - - +
574A TYR 3.4 23.8 - - - +
575A ASN* 3.7 18.0 + - + +
620A VAL* 4.2 26.9 - - + +
621A ASN* 3.8 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A PHE* 3.7 24.6 - - + -
532A GLY* 3.0 24.8 - - - -
553A MET* 4.0 9.0 - - + +
556A GLY 4.3 3.1 - - - -
557A LEU* 1.3 76.7 - - - +
559A ASP* 1.3 69.2 + - - +
573A SER* 3.3 4.6 - - - -
574A TYR* 2.8 41.0 + - + +
576A ILE* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A THR* 3.6 1.2 + - - +
531A PHE* 3.4 1.5 - - - -
532A GLY* 2.8 31.0 + - - +
533A GLY 4.7 0.5 + - - -
558A THR* 1.3 83.2 + - - +
560A VAL* 1.3 63.1 + - - +
561A LYS* 4.0 1.9 + - - +
571A LEU* 3.8 42.0 - - + +
572A TYR 3.7 1.6 - - - -
573A SER* 4.1 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ILE* 3.7 7.5 - - + +
504A VAL* 4.0 20.4 - - + -
517A ILE* 3.8 28.7 - - + -
529A VAL* 4.0 7.4 - - + -
530A THR 3.3 8.1 - - - +
531A PHE* 3.8 36.3 - - + -
558A THR 4.9 0.2 - - - +
559A ASP* 1.3 73.2 - - - +
561A LYS* 1.3 64.5 + - - +
571A LEU* 3.4 8.0 - - - -
572A TYR 2.8 38.3 + - - +
574A TYR* 3.9 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A ILE* 4.2 0.4 - - - -
528A THR 4.0 0.2 - - - +
529A VAL* 3.3 5.2 - - - +
530A THR* 2.9 50.1 + - - +
533A GLY* 6.4 0.4 - - - -
559A ASP 5.0 1.6 - - - +
560A VAL* 1.3 78.5 - - - +
562A VAL* 1.3 73.1 + - - +
563A THR* 4.3 9.2 + - - -
568A SER* 3.7 24.6 + - - +
569A SER* 3.8 16.4 - - - +
571A LEU* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A PRO* 3.9 9.8 - - + +
501A ILE* 3.9 21.3 - - + -
517A ILE* 4.0 18.6 - - + -
522A PHE* 3.9 16.2 - - + -
528A THR 3.5 2.5 - - - -
529A VAL* 4.4 2.2 - - + +
541A TRP* 3.8 25.6 - - + -
546A ILE* 3.9 22.2 - - + -
561A LYS* 1.3 77.3 - - - +
563A THR* 1.3 67.0 + - - +
564A ALA* 4.6 0.7 - - + +
567A VAL 3.9 0.7 - - - +
568A SER* 3.4 2.3 - - - -
569A SER* 2.8 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLY* 3.4 5.0 - - - -
528A THR* 2.8 53.6 + - - +
530A THR* 5.6 1.2 + - - +
541A TRP* 3.7 2.1 - - - -
561A LYS* 4.3 11.1 + - - -
562A VAL* 1.3 75.4 + - - +
564A ALA* 1.3 63.1 + - - +
566A GLY* 4.0 24.0 - - - +
567A VAL 3.3 12.1 - - - +
568A SER* 3.9 12.7 - - - +
----------------------------------------------------------
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