Contacts of the strand formed by residues 96 - 102 (chain A) in PDB entry 1DXO
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 96 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG 3.1 2.0 + - - -
5A ALA* 3.2 3.6 - - + -
6A LEU 2.9 24.3 + - - -
29A LEU* 4.2 14.6 - - + -
34A TRP* 3.5 25.8 - - + -
94A ALA* 3.7 1.2 - - - +
95A ASP* 1.3 78.4 - - - +
97A VAL* 1.3 66.9 + - - +
98A ILE* 4.2 26.0 - - + -
141A LYS* 3.4 25.8 - - + +
143A VAL* 3.7 23.6 - - + -
184A LEU* 4.4 7.4 - - + -
211A LEU* 4.7 1.3 - - + -
214A ILE* 3.9 26.7 - - + -
215A TRP* 4.1 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.3 20.2 - - + +
8A VAL* 4.5 2.2 - - + -
91A LEU* 4.2 11.4 - - + -
94A ALA* 3.7 22.4 - - + +
96A LEU* 1.3 80.5 - - - +
98A ILE* 1.3 67.0 + - - +
99A PHE* 3.7 33.1 - - + -
115A TRP* 5.6 0.2 - - + -
140A LYS* 5.2 0.7 - - + -
141A LYS 3.0 7.6 + - - +
142A ALA* 3.3 2.8 - - - +
143A VAL* 3.0 26.3 + - - +
181A PHE* 3.9 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ALA* 5.8 0.9 - - + -
6A LEU 2.9 12.6 + - - +
7A ILE* 3.4 17.2 - - + -
8A VAL* 2.7 35.5 + - - +
25A ALA* 4.3 12.3 - - + -
29A LEU* 4.2 13.2 - - + -
96A LEU* 4.2 19.3 - - + -
97A VAL* 1.3 77.8 - - - +
99A PHE* 1.3 68.0 + - - +
100A GLN* 4.3 4.3 - - + +
143A VAL* 3.5 15.0 - - + +
145A SER* 4.4 7.0 - - - -
207A TRP* 4.0 23.1 - - + -
211A LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.5 28.3 - - + -
91A LEU* 6.1 0.2 - - + -
97A VAL* 3.7 23.3 - - + -
98A ILE* 1.3 75.0 - - - +
100A GLN* 1.3 59.7 + - - +
101A PHE* 3.4 13.3 - - + -
112A LEU* 4.2 13.9 - - + -
115A TRP* 3.6 29.2 - + - -
116A PHE* 3.7 23.8 - + - -
120A PHE* 4.9 3.8 - + - -
142A ALA* 4.3 5.8 - - + -
143A VAL 2.9 14.0 + - - -
144A LEU* 3.5 29.5 - - + -
145A SER 2.9 26.5 + - - +
176A LEU* 3.8 25.8 - - + -
181A PHE* 5.4 2.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.8 11.9 - - + -
8A VAL 3.0 10.5 + - - +
9A LEU* 3.4 14.6 - - + +
10A ALA* 3.1 21.1 + - - +
18A ASN* 2.6 47.4 + - - +
21A MET* 3.0 27.4 - - + +
22A LYS* 4.5 4.7 - - + +
98A ILE* 3.8 4.7 - - + +
99A PHE* 1.3 70.6 - - - +
101A PHE* 1.3 77.2 + - - +
112A LEU* 5.7 0.2 - - - +
145A SER* 2.8 35.7 + - - -
147A THR* 4.4 9.7 - - - +
207A TRP* 4.6 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 3.9 18.8 - - + +
18A ASN* 3.1 8.0 - - - +
99A PHE* 3.4 16.8 - - + -
100A GLN* 1.3 83.6 - - - +
102A PRO* 1.3 92.8 - - + +
103A LEU* 4.5 2.2 - - + -
107A GLY 4.0 4.9 - - - -
108A VAL* 3.6 34.8 - - + -
109A PRO* 3.3 13.5 - - + -
112A LEU* 4.0 9.4 - - + -
144A LEU* 3.7 28.3 - - + -
145A SER 3.2 2.2 + - - -
146A ILE* 3.3 56.6 - - + -
147A THR 3.4 1.6 + - - -
171A ILE* 5.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 3.4 18.6 - - - +
11A HIS* 3.9 14.1 - - + -
18A ASN* 3.5 15.0 - - - +
101A PHE* 1.3 101.5 - - + +
103A LEU* 1.3 63.7 + - - +
104A GLN* 3.4 28.3 + - - +
109A PRO* 3.8 3.1 - - + +
147A THR* 3.1 11.7 - - - +
301A FAD 3.1 33.4 - - - +
----------------------------------------------------------
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