Contacts of the strand formed by residues 163 - 171 (chain D) in PDB entry 1DVM
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 163 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LEU* 5.2 4.5 - - + -
49D THR* 5.2 0.4 - - - +
97D ILE* 3.9 21.5 - - + -
98D PHE 3.3 13.0 - - - +
99D VAL* 4.2 7.0 - - + -
126D PHE* 4.0 1.6 - - - -
161D THR* 4.2 0.2 - - - +
162D ARG* 1.3 80.3 - - - +
164D VAL* 1.3 68.4 + - - +
165D LEU* 6.5 0.2 - - + -
306D PHE* 4.0 24.7 - - + -
309D LEU* 3.9 21.3 - - + -
315D LEU* 3.4 13.2 - - + -
316D HIS 3.1 31.7 + - - +
317D VAL* 3.9 19.0 - - + -
318D ALA* 3.1 24.3 + - - +
319D LEU 3.6 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D ALA 3.8 0.3 - - - +
97D ILE* 3.1 7.2 - - - +
98D PHE* 2.7 52.4 + - + +
126D PHE* 3.7 25.1 - - + -
136D ILE* 4.8 9.9 - - + -
157D VAL* 4.8 4.0 - - + -
161D THR* 3.7 15.0 - - + -
163D LEU* 1.3 80.3 - - - +
165D LEU* 1.3 70.1 + - - +
166D VAL* 3.9 16.4 - - + -
319D LEU* 3.4 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 3.6 44.9 - - + +
43D LEU* 5.0 4.3 - - + -
46D LEU* 5.0 20.4 - - + -
96D ALA 3.6 2.7 - - - +
97D ILE* 3.5 30.1 - - + +
164D VAL* 1.3 75.5 - - - +
166D VAL* 1.3 76.8 + - - +
286D LEU* 4.3 6.5 - - + -
298D MET* 6.5 0.4 - - + -
317D VAL* 4.7 7.3 - - + +
319D LEU 2.7 14.6 + - - +
320D ALA* 4.1 18.2 - - + -
321D LEU* 3.1 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D VAL* 3.6 5.2 - - - +
94D THR* 5.6 2.5 - - + +
95D ASP* 3.7 0.4 - - - -
96D ALA* 2.8 47.9 + - + +
98D PHE* 4.9 2.5 - - + -
136D ILE* 4.2 13.0 - - + -
139D TRP* 6.1 0.2 - - + -
140D VAL* 4.1 16.8 - - + -
151D LEU* 3.6 33.9 - - + -
164D VAL* 3.9 17.3 - - + -
165D LEU* 1.3 85.7 - - - +
167D ASN* 1.3 71.5 + - - +
168D ALA* 4.7 1.8 - - + +
319D LEU* 5.6 0.2 - - + -
321D LEU* 3.7 16.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D GLY* 3.1 23.4 + - - -
39D VAL* 3.5 0.4 + - - -
42D VAL* 3.6 13.7 - - + -
94D THR 3.5 8.4 + - - -
95D ASP* 2.8 27.9 + - - -
151D LEU* 6.0 0.2 - - - +
166D VAL* 1.3 79.9 - - - +
168D ALA* 1.3 61.5 + - - +
169D LEU* 3.1 17.7 - - - +
286D LEU* 5.6 0.7 - - + -
321D LEU 3.2 12.0 + - - +
322D GLN* 3.0 56.9 + - + +
323D LYS 3.0 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D THR* 3.4 4.3 - - - -
94D THR* 3.0 38.5 + - + +
140D VAL* 3.6 33.9 - - + -
144D THR* 3.9 4.8 - - + +
148D ILE* 4.1 15.0 - - + -
151D LEU* 5.0 2.7 - - + -
166D VAL* 5.1 0.9 - - + -
167D ASN* 1.3 75.6 - - - +
169D LEU* 1.3 61.4 + - - +
323D LYS* 3.2 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D SER* 3.2 32.8 - - - +
37D TYR* 5.0 9.0 - - + -
38D GLY* 4.2 8.7 - - - +
91D ILE* 5.5 0.2 - - + -
92D SER 3.8 4.3 - - - -
93D THR* 3.2 32.3 - - + +
95D ASP* 5.6 0.9 - - - +
148D ILE* 3.2 7.5 - - - +
167D ASN* 3.1 32.8 - - - +
168D ALA* 1.3 80.1 - - - +
170D TYR* 1.3 60.3 + - - +
322D GLN* 4.2 0.7 - - + -
323D LYS 3.1 4.0 + - - -
324D VAL* 3.2 14.0 - - + -
325D LYS 3.0 23.3 + - - -
372D PHE* 3.4 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ASP 4.6 9.0 - - - -
90D GLU 4.1 7.2 - - - -
91D ILE* 3.2 26.5 - - - +
92D SER* 3.0 28.9 + - - +
144D THR* 5.2 0.4 - - - -
147D MET* 3.2 50.5 - - + +
148D ILE* 4.0 6.1 - - + -
169D LEU* 1.3 76.6 - - - +
171D PHE* 1.3 67.8 + - - +
172D ASN* 3.3 33.6 + - + +
325D LYS* 3.1 32.5 - - + -
327D GLU* 2.6 31.6 + - + -
372D PHE* 4.2 0.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D GLU* 3.1 13.7 - - + -
91D ILE* 3.9 10.8 - - + -
170D TYR* 1.3 82.2 - - - +
172D ASN* 1.3 74.1 - - - +
173D GLY* 3.7 21.1 - - - -
228D TYR* 3.3 40.8 - + - -
233D LEU* 3.6 24.2 - - + -
235D MET* 5.0 1.3 - - + -
325D LYS 2.7 10.0 + - - +
326D ILE* 3.5 24.9 - - + -
327D GLU 2.9 25.5 + - - -
362D VAL* 3.8 23.6 - - + -
371D LEU* 5.4 0.7 - - + -
372D PHE* 3.8 33.9 - + + -
----------------------------------------------------------
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