Contacts of the helix formed by residues 88 - 98 (chain A) in PDB entry 1D0L
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 LEU 88 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS* 3.8 41.1 - - + +
87A ARG* 1.3 70.8 - - - +
89A ASP* 1.3 67.7 + - - +
90A SER* 3.1 8.3 - - - +
91A VAL* 3.0 36.3 + - + +
92A LEU* 3.4 3.9 + - - -
172A THR* 3.6 31.4 - - + -
176A ASP* 3.6 16.4 - - + +
177A ALA 4.3 2.5 - - - +
180A THR* 2.9 18.6 + - - +
217A PHE* 5.7 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 3.3 42.2 + - - +
88A LEU* 1.3 71.8 - - - +
90A SER* 1.3 57.9 + - - +
92A LEU* 3.0 20.3 + - + +
93A ARG* 2.9 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 4.2 11.6 - - - +
89A ASP* 1.3 76.8 - - - +
91A VAL* 1.3 62.7 + - - +
93A ARG* 3.5 30.0 + - - +
94A LEU* 3.0 39.8 + - - +
217A PHE* 4.4 13.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A LEU* 3.0 39.9 + - + +
90A SER* 1.3 81.9 + - - +
92A LEU* 1.3 57.5 + - - +
94A LEU* 3.5 4.6 + - - +
95A MET* 3.1 30.4 + - + +
172A THR* 4.8 0.2 - - + -
177A ALA* 4.4 7.4 - - - +
180A THR* 4.4 7.6 - - + -
181A LEU* 3.7 26.7 - - + -
217A PHE* 3.3 52.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A ARG* 4.6 4.7 - - + -
88A LEU 3.8 1.8 - - - +
89A ASP* 3.0 30.2 + - + +
91A VAL* 1.3 75.4 - - - +
93A ARG* 1.3 64.8 + - + +
95A MET* 3.5 5.5 + - - +
96A ASP* 3.2 31.1 + - - +
180A THR* 3.6 30.3 - - + +
181A LEU* 4.5 4.5 - - + -
184A ASN* 3.4 36.1 - - + +
185A TYR* 3.8 24.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP* 2.9 36.9 + - + +
90A SER* 3.6 29.4 - - - +
92A LEU* 1.3 76.4 - - + +
94A LEU* 1.3 60.8 + - + +
96A ASP* 3.3 8.1 + - - +
97A ASN* 3.0 39.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A SER* 3.0 24.6 + - - +
91A VAL* 3.9 4.0 - - - +
92A LEU 3.3 0.2 - - - -
93A ARG* 1.3 75.0 - - + +
95A MET* 1.3 62.0 + - + +
97A ASN* 3.2 15.6 + - + +
98A GLN* 3.0 44.3 + - + +
217A PHE* 3.5 48.7 - - + -
401A BLG 5.6 4.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A VAL* 3.1 19.3 + - + +
92A LEU 3.8 2.9 - - - +
94A LEU* 1.3 78.2 - - + +
96A ASP* 1.3 59.7 + - - +
98A GLN* 3.8 18.2 + - - +
99A ALA 3.4 8.5 + - - -
181A LEU* 3.9 32.5 - - + -
185A TYR* 3.2 46.2 + - + +
187A ARG* 3.2 16.3 + - - +
188A ARG* 3.7 26.0 - - - +
192A PHE* 4.4 3.4 - - + -
217A PHE* 4.6 7.2 - - + +
218A ALA* 4.3 18.2 - - + -
401A BLG 5.4 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 3.2 20.9 + - - +
93A ARG* 3.5 11.7 - - - +
94A LEU 3.1 0.6 - - - -
95A MET* 1.3 75.5 - - - +
97A ASN* 1.3 67.9 + - - +
98A GLN 3.1 2.0 - - - -
99A ALA* 3.1 21.4 + - - +
185A TYR* 3.2 24.6 + - - -
187A ARG* 5.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ARG* 3.0 28.1 + - - +
94A LEU* 3.2 18.0 + - + +
96A ASP* 1.3 80.1 - - - +
98A GLN* 1.3 61.7 + - + +
99A ALA 3.3 4.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A LEU* 3.0 25.9 + - + +
95A MET* 3.8 19.7 + - - +
97A ASN* 1.3 79.4 - - + +
99A ALA* 1.3 62.3 + - - +
100A PRO* 3.6 5.5 - - - +
187A ARG* 5.1 0.6 + - - -
401A BLG 4.0 36.5 + - - +
----------------------------------------------------------
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