Contacts of the strand formed by residues 552 - 559 (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 SER 552 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545A LEU* 3.8 6.1 - - - -
550A LEU* 3.4 25.5 + - - +
551A PRO* 1.3 86.4 - - - +
553A LYS* 1.3 62.8 + - - +
554A HIS* 5.2 5.3 + - - -
633A VAL* 3.9 11.1 - - - +
634A LEU 3.0 14.1 - - - -
635A THR* 3.7 17.0 - - - -
937A ASN 4.7 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 553 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ILE* 3.6 36.3 - - + +
544A ILE 5.8 0.7 - - - +
545A LEU* 4.2 2.7 - - + -
550A LEU* 4.0 22.4 - - - +
552A SER* 1.3 74.9 - - - +
554A HIS* 1.3 82.8 + - - +
555A VAL* 3.8 1.1 + - + -
633A VAL* 3.4 2.2 - - - -
634A LEU* 2.9 42.9 + - + +
933A ILE* 4.0 15.9 - - + -
934A PHE* 2.8 31.7 + - + +
935A ALA 3.7 7.1 + - - -
936A GLU 2.9 24.0 + - - -
937A ASN* 4.6 1.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 554 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552A SER* 5.2 3.9 + - - -
553A LYS* 1.3 83.6 + - - +
555A VAL* 1.3 63.2 - - - +
556A VAL* 5.5 0.7 - - - -
583A LEU* 3.6 17.5 - - + +
631A THR* 3.8 22.2 - - + -
632A TYR 3.3 4.7 - - - +
633A VAL* 3.7 21.4 - - + +
934A PHE* 3.0 34.3 + - + +
939A TRP* 3.9 40.2 + + + +
942A ALA* 4.3 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 555 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543A ILE* 4.0 22.0 - - + -
553A LYS* 3.8 3.8 + - + +
554A HIS* 1.3 77.9 - - - +
556A VAL* 1.3 65.2 + - - +
557A MET* 4.1 6.2 - - + +
571A PHE* 3.8 41.5 - - + -
620A PHE* 4.3 4.0 - - + -
631A THR* 3.4 4.3 - - - +
632A TYR* 2.8 54.6 + - + +
634A LEU* 4.5 12.3 - - + -
932A PHE 3.2 11.2 - - - +
933A ILE* 4.3 3.6 - - + -
934A PHE 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A VAL* 3.9 9.9 - - + -
509A LEU* 3.6 20.9 - - + -
524A PHE* 3.9 9.9 - - + -
555A VAL* 1.3 80.8 - - - +
557A MET* 1.3 74.9 + - - +
629A LEU* 3.9 15.5 - - + -
630A ALA 3.4 9.4 - - - +
631A THR* 3.8 10.5 - - + +
931A LYS* 3.5 1.9 - - - -
932A PHE* 2.8 47.3 + - + -
939A TRP* 3.7 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555A VAL* 4.1 8.1 - - + -
556A VAL* 1.3 86.2 - - - +
558A HIS* 1.4 59.2 + - - +
569A VAL* 3.9 22.9 - - + -
571A PHE* 3.9 23.8 - - - -
620A PHE* 4.0 16.6 - - + -
622A ALA* 4.0 4.9 - - + -
624A VAL* 3.7 21.6 - - + +
629A LEU* 3.2 7.1 - - - +
630A ALA 2.9 33.2 + - - +
632A TYR* 3.5 34.3 - - + -
929A LEU* 4.0 11.0 - - + -
930A ASP 3.1 9.6 - - - +
931A LYS* 3.9 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ALA* 4.1 10.1 - - + -
441A MET* 4.3 11.6 - - - +
442A LEU* 3.5 43.1 - - + +
445A TRP* 5.7 0.8 + - - -
556A VAL 4.3 0.2 + - - -
557A MET* 1.4 73.2 - - - +
559A ASN* 1.3 63.1 + - - +
560A THR* 3.7 35.1 + - - -
627A MET 4.6 4.6 + - - -
628A GLY* 3.2 25.8 - - - -
629A LEU* 3.5 11.7 - - + -
929A LEU* 3.2 10.9 - - - +
930A ASP* 2.8 53.6 + - + +
932A PHE* 3.9 14.5 - - + -
946A PHE* 6.3 0.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A HIS* 1.3 75.8 - - - +
560A THR* 1.3 57.8 + - - +
561A LEU* 3.2 14.1 + - - +
563A HIS 2.8 29.1 + - - -
565A ARG* 2.9 42.0 + - - +
624A VAL* 3.5 27.1 + - + +
625A PRO 3.0 15.8 + - - +
627A MET* 3.0 28.4 + - - -
628A GLY 3.0 8.6 + - - -
929A LEU* 3.6 9.6 - - + -
----------------------------------------------------------
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