Contacts of the strand formed by residues 163 - 172 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.9 4.3 - - + -
97A ILE* 3.8 24.7 - - + -
98A PHE 3.1 18.4 - - - +
99A VAL* 4.3 4.3 - - + -
126A PHE* 3.9 1.6 - - - -
161A THR* 4.0 0.2 - - - +
162A ARG* 1.3 82.5 - - - +
164A VAL* 1.3 71.6 + - - +
306A PHE* 4.1 21.3 - - + -
309A LEU* 4.2 19.1 - - + -
315A LEU* 3.8 13.0 - - + -
316A HIS 3.5 15.5 + - - +
317A VAL* 3.8 33.2 - - + +
318A ALA* 2.8 29.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ALA 4.4 0.2 - - - -
97A ILE* 3.4 9.5 - - - +
98A PHE* 2.8 44.9 + - + +
126A PHE* 4.2 6.3 - - + -
136A ILE* 4.6 8.3 - - + -
154A THR* 6.0 0.4 - - + -
157A VAL* 4.2 14.6 - - + -
161A THR* 3.8 21.3 - - + -
163A LEU* 1.3 83.1 - - - +
165A LEU* 1.3 62.4 - - - +
166A VAL* 3.7 25.1 - - + -
317A VAL* 4.7 1.3 - - - -
319A LEU* 3.4 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.6 42.8 - - + +
43A LEU* 5.0 5.2 - - + -
46A LEU* 4.9 15.9 - - + -
96A ALA 3.6 2.5 - - - +
97A ILE* 4.0 25.4 - - + +
164A VAL* 1.3 72.7 - - - +
166A VAL* 1.3 78.2 + - - +
286A LEU* 4.3 6.7 - - + -
317A VAL* 4.3 7.8 - - + +
319A LEU 2.6 23.2 + - - +
320A ALA* 3.8 15.3 - - + -
321A LEU* 3.2 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.7 5.5 - - - +
94A THR* 5.2 2.7 - - + +
95A ASP* 3.6 2.8 - - - -
96A ALA* 2.9 40.7 + - + +
98A PHE* 4.6 6.1 - - + -
136A ILE* 4.1 17.7 - - + -
140A VAL* 3.8 28.7 - - + -
151A LEU* 4.2 10.3 - - + -
154A THR* 5.6 0.7 - - + -
164A VAL* 3.7 18.4 - - + -
165A LEU* 1.3 84.4 - - - +
167A ASN* 1.3 72.0 + - - +
168A ALA* 4.8 1.6 - - + +
321A LEU* 3.7 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A GLY* 3.0 33.5 - - - -
42A VAL* 3.7 15.3 - - + +
94A THR 3.5 5.1 + - - +
95A ASP* 2.6 30.3 + - - -
151A LEU* 5.7 0.2 - - - +
165A LEU* 5.0 0.2 - - + -
166A VAL* 1.3 80.4 - - - +
168A ALA* 1.3 62.8 + - - +
169A LEU* 3.4 18.5 - - - +
286A LEU* 5.6 0.4 - - + -
321A LEU* 3.2 12.2 + - - +
322A GLN* 3.0 24.5 + - + +
323A LYS* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A THR* 3.2 4.9 - - - -
94A THR* 3.0 40.2 + - + +
140A VAL* 3.6 34.1 - - + -
144A THR* 3.9 2.7 - - + +
148A ILE* 3.9 10.3 - - + -
151A LEU* 5.9 0.7 - - + -
166A VAL* 5.1 1.1 - - + -
167A ASN* 1.3 77.9 - - - +
169A LEU* 1.3 62.4 - - - +
323A LYS* 3.2 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A SER* 3.6 29.6 - - - +
37A TYR* 4.7 13.2 - - + -
38A GLY* 4.2 2.5 - - - -
91A ILE* 4.5 3.1 - - + -
92A SER 3.4 6.5 - - - -
93A THR* 3.2 31.6 - - + -
148A ILE* 3.0 10.8 - - - +
167A ASN* 3.4 35.2 - - - +
168A ALA* 1.3 82.2 - - - +
170A TYR* 1.3 60.7 + - - +
323A LYS 3.0 8.4 + - - +
324A VAL* 3.5 6.0 - - + -
325A LYS 3.0 23.4 + - - -
372A PHE* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP 4.5 9.2 - - - -
90A GLU 3.3 6.4 - - - +
91A ILE* 3.1 8.5 - - - +
92A SER* 2.9 40.4 + - - +
144A THR* 5.1 0.9 - - - +
147A MET* 3.6 55.9 - - + +
148A ILE* 4.6 1.8 - - + -
169A LEU* 1.3 77.0 - - - +
171A PHE* 1.3 60.4 + - - +
172A ASN* 3.3 37.8 + - + +
325A LYS* 3.4 25.6 - - + -
327A GLU* 2.7 36.7 + - + -
372A PHE* 4.6 1.6 - - - -
347D MET* 4.5 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 3.1 22.0 - - + -
91A ILE* 3.9 8.1 - - + -
170A TYR* 1.3 76.2 - - - +
172A ASN* 1.3 67.1 + - - +
173A GLY* 4.1 13.2 - - - -
228A TYR* 3.3 42.6 - + - -
233A LEU* 3.5 26.2 - - + -
235A MET* 4.7 2.0 - - + -
325A LYS 2.8 10.8 + - - +
326A ILE* 3.6 23.9 - - + +
327A GLU* 2.9 32.3 + - - +
362A VAL* 4.0 18.8 - - + -
372A PHE* 3.5 35.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ASP 5.0 1.6 - - - +
90A GLU* 2.7 32.0 + - - +
170A TYR* 3.3 32.2 + - + +
171A PHE* 1.3 75.9 - - - +
173A GLY* 1.3 71.0 + - - +
174A GLN* 4.7 0.9 - - - +
327A GLU* 3.6 25.9 + - - +
328A VAL* 4.9 0.4 - - - +
329A ASN* 3.7 25.4 + - - +
331A SER* 5.3 1.0 + - - -
----------------------------------------------------------
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