Contacts of the strand formed by residues 629 - 634 (chain A) in PDB entry 2ZT5
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 629 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A ASP* 4.4 3.4 + - - +
622A THR* 2.6 32.2 + - - +
625A LYS* 6.0 0.2 - - - +
627A PRO* 3.2 19.1 + - + +
628A HIS* 1.3 78.6 - - - +
630A ALA* 1.3 54.9 + - - +
642A ARG* 2.8 44.2 + - + +
643A ALA* 3.2 11.9 - - - -
644A GLU* 3.8 18.6 - - + +
645A ILE 4.4 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 630 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A VAL* 3.7 9.6 - - + -
617A THR 3.4 14.6 - - - +
618A ILE* 4.5 0.4 - - + -
622A THR* 3.9 4.5 - - + -
629A THR* 1.3 75.2 - - - +
631A THR* 1.3 61.6 + - - +
632A LEU 4.0 0.2 + - - -
641A ILE 3.7 0.2 - - - +
642A ARG* 3.3 11.0 - - - -
643A ALA 2.8 29.5 + - - +
645A ILE* 4.1 18.8 - - + +
648A LEU* 3.5 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 631 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615A GLY 3.4 1.0 - - - +
616A VAL* 3.0 8.6 - - - +
617A THR* 2.7 50.5 + - - +
619A ASP* 4.2 2.3 + - - -
630A ALA* 1.3 72.4 - - - +
632A LEU* 1.3 62.2 + - - +
640A GLN* 3.4 45.1 - - + +
641A ILE 3.1 11.7 - - - +
642A ARG* 2.6 26.2 + - - -
648A LEU* 5.0 0.4 - - - -
672A PHE* 3.3 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 632 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A PHE* 4.5 12.6 - - + -
615A GLY 3.4 15.0 - - - +
616A VAL* 4.1 8.5 - - + +
630A ALA 4.0 1.0 + - - -
631A THR* 1.3 73.2 - - - +
633A ARG* 1.3 61.1 + - - +
640A GLN* 3.1 6.4 - - - +
641A ILE* 2.8 41.6 + - + -
648A LEU* 3.9 20.6 - - + -
651A ILE* 3.8 29.6 - - + -
652A VAL* 3.9 24.0 - - + -
655A LEU* 3.9 6.1 - - + -
662A TRP* 3.8 27.7 - - + -
665A VAL* 4.3 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 633 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601A GLY 5.8 0.6 + - - -
604A TYR* 3.5 56.6 - - + +
607A THR* 5.4 1.6 - - - +
608A ASP* 3.1 37.8 + - - -
614A PHE* 3.5 10.1 - - - +
615A GLY 2.8 34.8 + - - +
631A THR* 5.3 0.2 - - + -
632A LEU* 1.3 76.6 - - - +
634A ASP* 1.3 65.8 + - - +
635A ARG* 3.6 10.9 + - - +
638A MET* 3.2 46.4 + - - +
639A ARG 3.6 4.7 - - - +
640A GLN* 3.7 26.7 - - + +
662A TRP* 4.2 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 634 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A ALA 4.5 0.7 - - - +
614A PHE* 3.6 22.4 - - - -
633A ARG* 1.3 75.0 - - - +
635A ARG* 1.3 59.0 + - - +
636A ASP* 3.7 12.1 + - - +
637A SER* 2.8 41.0 + - - +
638A MET* 2.7 34.5 + - - -
639A ARG 3.0 6.9 + - - -
662A TRP* 3.4 39.9 - - + +
----------------------------------------------------------
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