Contacts of the helix formed by residues 74 - 79 (chain K) in PDB entry 1ZUM
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 74 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68K ALA 4.3 6.1 - - - -
69K ALA* 2.8 32.3 + - - -
71K GLN* 2.9 23.6 + - - +
72K LEU 3.3 1.0 + - - -
73K GLY* 1.3 80.4 - - - +
75K PRO* 1.3 75.5 - - - +
76K TRP 3.7 0.2 + - - -
77K ARG* 3.3 11.3 + - - +
78K ARG* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 75 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69K ALA* 6.3 0.7 - - - -
73K GLY 4.7 0.4 - - - +
74K SER* 1.3 87.2 - - - +
76K TRP* 1.3 56.6 + - - +
78K ARG* 3.5 4.1 + - + -
79K MET* 3.0 37.2 + - + +
214K PRO* 4.3 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 76 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500J SER* 4.6 4.0 + - - -
69K ALA* 3.8 14.8 - - + +
74K SER* 3.3 1.0 + - - -
75K PRO* 1.3 80.7 - - - +
77K ARG* 1.3 64.3 + - - +
79K MET* 3.6 41.2 - - - +
84K ARG* 3.7 27.9 - - + -
87K LEU* 3.8 14.8 - - + -
88K LEU* 6.4 0.2 - - + -
183K LEU* 3.5 26.0 - - + -
186K GLY* 3.2 21.3 + - - -
187K ASN 3.0 20.9 + - - -
188K VAL* 3.8 20.0 - - + -
213K PHE* 3.8 23.1 - + - -
214K PRO* 3.8 17.8 - - + +
217K VAL* 3.6 29.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 77 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498J LYS* 6.0 0.2 - - - -
499J ASN* 3.3 20.2 - - - +
500J SER* 2.8 72.7 + - - -
70K PHE* 2.7 82.9 + - - +
71K GLN 3.4 6.7 - - - +
72K LEU* 3.7 29.7 - - - +
73K GLY 4.3 0.2 - - - +
74K SER* 3.3 20.0 + - - +
76K TRP* 1.3 81.3 - - - +
78K ARG* 1.3 61.8 + - - +
79K MET 4.2 2.6 - - - +
157K GLU* 5.7 3.2 - - - -
158K PRO* 4.8 2.2 - - - +
186K GLY 4.6 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J ASP* 4.0 21.2 + - - -
497J GLN* 3.4 39.4 - - - +
498J LYS* 3.7 24.6 + - - +
499J ASN* 3.6 15.3 - - - +
73K GLY* 3.5 19.9 + - - +
74K SER 3.0 17.1 + - - +
75K PRO* 4.2 3.8 - - + +
77K ARG* 1.3 75.0 - - - +
79K MET* 1.3 66.0 + - - +
80K ASP* 3.6 3.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 79 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498J LYS* 4.7 4.0 - - - -
500J SER* 5.5 1.2 + - - -
75K PRO* 3.0 24.6 + - + +
76K TRP* 3.6 36.1 - - + +
77K ARG 3.4 4.9 - - - +
78K ARG* 1.3 78.6 - - - +
80K ASP* 1.3 72.0 + - - +
81K ALA* 3.5 1.6 + - - -
83K HIS* 3.4 41.1 - - + +
84K ARG* 4.1 15.0 + - + -
87K LEU* 3.7 12.3 - - + -
212K GLY 5.4 1.1 - - - +
214K PRO* 4.0 27.4 - - + -
----------------------------------------------------------
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