Contacts of the helix formed by residues 103 - 113 (chain A) in PDB entry 1DZA
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 103 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A FME 3.9 14.4 + - - +
101A LYS 4.1 1.0 - - - -
102A GLU* 1.3 77.5 - - - +
104A ALA* 1.3 60.8 + - - +
105A ALA* 3.5 8.1 + - - +
106A ALA* 2.8 27.4 + - - +
107A LYS* 2.9 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A FME 3.6 18.4 - - + +
103A SER* 1.3 73.7 - - - +
105A ALA* 1.3 64.3 + - - +
107A LYS* 3.2 9.5 + - - +
108A PHE* 3.0 23.4 + - - +
218A VAL* 3.6 32.7 - - + +
176B ASN* 4.8 13.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A SER* 3.2 7.9 + - - +
104A ALA* 1.3 78.9 - - - +
106A ALA* 1.3 62.7 + - - +
108A PHE* 3.2 5.9 + - - +
109A GLU* 3.0 21.7 + - - +
216A VAL* 4.1 23.6 - - + -
217A PRO 4.1 11.9 - - - +
218A VAL* 4.4 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 3.9 16.3 - - + +
103A SER* 2.8 24.5 + - - +
105A ALA* 1.3 77.8 - - - +
107A LYS* 1.3 56.1 + - - +
109A GLU* 3.3 9.8 + - - +
110A ARG* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 3.7 19.2 + - + +
103A SER 2.9 13.4 + - - +
104A ALA* 3.2 11.4 + - - +
106A ALA* 1.3 73.5 - - - +
108A PHE* 1.3 61.6 + - - +
110A ARG* 3.2 20.1 + - - +
111A GLN* 2.9 60.4 + - - +
218A VAL 5.8 4.0 - - - +
158B CYS 4.5 0.4 + - - -
159B PHE* 3.2 28.4 + - - +
160B GLN 2.7 30.4 + - - +
161B GLU* 5.2 0.9 - - - -
162B LYS* 5.0 8.7 - - - +
173B TYR* 4.3 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ALA 3.0 10.8 + - - +
105A ALA 3.5 9.4 - - - +
107A LYS* 1.3 77.9 - - - +
109A GLU* 1.3 68.1 + - + +
111A GLN* 5.6 0.7 - - - +
112A HIS* 2.8 53.8 + + + +
113A MET* 4.0 18.2 - - + -
147A VAL* 5.6 1.1 - - + -
151A LEU* 4.9 7.0 - - + -
154A VAL* 3.8 25.6 - - + -
208A VAL* 4.2 7.2 - - + -
217A PRO* 3.6 41.3 - - + +
218A VAL* 3.8 7.8 + - - -
219A HIS 3.7 37.2 - - - -
220A PHE* 3.8 10.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 3.0 12.8 + - - +
106A ALA* 3.3 11.7 + - - +
108A PHE* 1.3 79.7 - - + +
110A ARG* 1.3 62.2 + - - +
113A MET* 3.0 44.0 + - + +
133A ARG* 3.4 7.4 + - - -
151A LEU* 4.2 27.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 2.8 41.0 + - - +
106A ALA 3.0 15.6 + - - +
107A LYS* 3.2 22.7 + - - +
109A GLU* 1.3 76.4 - - - +
111A GLN* 1.3 75.9 + - - +
132A ARG 5.8 0.2 - - - -
133A ARG* 2.7 79.3 + - - +
134A ASN* 3.6 25.1 + - - +
135A MET* 4.8 0.8 - - - +
162B LYS* 5.0 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 2.9 48.5 + - + +
108A PHE* 5.6 0.6 - - - +
110A ARG* 1.3 95.9 + - - +
112A HIS* 1.4 90.6 + - + +
135A MET* 3.8 23.6 - - - +
141A LYS* 3.6 19.5 + - - +
144A ASN* 2.9 27.9 + - - -
146A PHE* 3.2 8.5 - - - -
219A HIS* 5.7 3.8 + - - -
159B PHE* 6.2 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 2.8 51.3 + + + +
111A GLN* 1.4 109.8 + - + +
113A MET* 1.3 55.9 + - - +
141A LYS* 4.1 5.6 - - - -
144A ASN* 3.1 23.8 - - - -
145A THR 2.9 26.3 + - - +
146A PHE* 3.3 4.9 - - - -
147A VAL* 2.7 37.0 + - + +
219A HIS* 5.1 4.9 + + - -
220A PHE* 3.5 38.2 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 4.0 18.8 - - + -
109A GLU* 3.0 39.7 + - + +
111A GLN 4.0 0.4 - - - -
112A HIS* 1.3 84.5 - - - +
114A ASP* 1.3 62.1 + - - +
115A SER* 4.0 4.5 - - - +
133A ARG* 2.9 30.1 + - - +
146A PHE* 4.6 0.2 - - - -
147A VAL* 4.0 10.3 - - - +
149A GLU 3.2 26.9 - - - +
151A LEU* 3.7 37.7 - - + +
154A VAL* 3.8 24.7 - - + -
----------------------------------------------------------
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