Contacts of the strand formed by residues 146 - 157 (chain D) in PDB entry 3VZC
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 146 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B GLU* 3.6 49.8 - - + +
7D GLY* 4.6 9.4 - - - +
9D GLY 3.5 3.8 - - - +
10D VAL* 3.5 21.5 - - + -
141D LEU 4.5 2.0 + - - -
144D ARG* 3.4 18.4 - - + +
145D ARG* 1.3 77.7 - - - +
147D LEU* 1.3 54.2 + - - +
362D VAL* 3.1 7.8 - - - +
363D SER 2.7 48.1 + - - +
364D GLY* 4.5 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLU* 5.5 0.4 - - - +
7D GLY* 3.7 0.9 - - - -
8D SER* 2.7 32.4 + - - -
9D GLY* 3.0 18.7 + - - -
10D VAL 3.6 32.5 - - - +
11D LEU* 3.9 11.4 - - + +
104D PRO* 3.9 28.9 - - + -
145D ARG 3.7 7.6 - - - +
146D LEU* 1.3 82.2 - - - +
148D SER* 1.3 60.6 + - - +
360D TRP* 3.7 22.4 - - + -
361D MET 3.2 4.5 - - - +
362D VAL* 3.8 26.9 - - + +
363D SER* 4.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 148 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D MET* 3.9 16.3 + - - +
7D GLY* 4.5 1.9 - - - -
8D SER* 4.5 1.1 + - - -
147D LEU* 1.3 75.4 + - - +
149D PRO* 1.3 72.2 - - - +
150D MET* 3.9 5.5 - - - +
279D ARG* 3.8 26.1 + - - -
360D TRP* 3.8 4.5 - - - -
361D MET* 2.8 31.2 + - - +
363D SER* 3.2 23.1 + - - -
364D GLY 5.7 1.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 149 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B MET* 4.5 13.5 - - + -
321B TYR* 5.6 2.0 - - + -
8D SER* 3.9 11.4 - - - +
148D SER* 1.3 87.9 - - - +
150D MET* 1.3 71.2 + - - +
279D ARG* 4.1 4.6 + - - +
357D ASN* 3.4 43.4 - - + +
359D PHE 3.2 9.9 - - - +
360D TRP* 3.6 37.6 - - + -
1002D EDO 4.7 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120D LEU* 4.6 8.1 - - - -
123D TYR* 4.7 1.1 - - + -
148D SER* 3.9 10.1 - - - +
149D PRO* 1.3 85.7 - - - +
151D ASN* 1.3 61.3 + - - +
265D HIS* 3.5 13.9 - - + +
279D ARG* 3.4 19.3 - - - +
357D ASN* 3.6 6.3 - - - -
358D TYR* 2.8 28.8 + - - -
359D PHE* 2.7 33.7 + - + +
361D MET* 3.7 46.0 - - + -
1002D EDO 2.8 52.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D MET* 1.3 78.3 - - - +
152D LEU* 1.3 58.3 + - - +
166D VAL* 4.7 2.3 - - - +
264D LEU* 3.5 20.7 - - + +
265D HIS* 5.1 0.9 + - - -
280D CYS* 4.2 0.8 - - - +
281D ALA 2.9 26.3 + - - -
282D ALA* 3.6 0.6 - - - +
283D GLY 2.9 21.9 + - - +
284D VAL 3.0 16.8 + - - +
354D VAL* 3.6 14.6 - - + -
355D HIS 3.4 4.5 - - - -
356D PRO* 3.3 0.9 - - - +
357D ASN* 3.0 22.7 + - - +
359D PHE* 3.5 12.3 - - - -
1002D EDO 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D VAL* 4.0 14.8 - - + -
92D MET* 4.2 17.7 - - + -
101D ILE* 4.7 4.3 - - + -
151D ASN* 1.3 75.3 - - - +
153D LEU* 1.3 63.4 - - - +
154D SER 3.9 0.2 + - - -
164D PHE* 3.4 44.0 - - + -
165D SER 3.3 24.5 - - - +
166D VAL* 4.3 2.5 - - + -
264D LEU* 4.0 3.6 - - - -
354D VAL* 3.5 2.5 - - - -
355D HIS* 2.8 35.8 + - + +
358D TYR* 4.0 35.2 - - + -
359D PHE* 4.2 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LEU* 1.3 72.5 - - - +
154D SER* 1.3 76.3 + - - +
155D LEU* 3.8 25.6 + - + +
164D PHE* 3.2 10.0 - - - +
165D SER* 2.8 60.1 + - - +
169D LEU* 4.7 6.3 - - + +
262D ALA* 4.7 3.8 - - + -
264D LEU* 4.0 10.7 - - + +
285D MET* 3.8 34.3 - - + -
327D PHE* 4.2 10.5 - - + -
352D GLY* 3.9 4.3 - - - -
353D GLN 3.4 22.4 - - - +
354D VAL* 4.5 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D LEU 3.9 2.0 + - - -
153D LEU* 1.3 74.1 - - - +
155D LEU* 1.3 58.4 + - - +
156D HIS* 3.7 1.8 + - - -
162D ARG* 2.7 25.7 + - - -
163D LEU 3.7 4.0 - - - -
164D PHE* 3.9 10.3 - - - -
235D ASP* 2.7 37.7 + - - -
352D GLY* 2.9 26.9 - - - -
353D GLN 2.9 15.6 + - - -
355D HIS* 3.8 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D LEU* 3.8 32.3 - - + +
154D SER* 1.3 75.3 + - - +
156D HIS* 1.3 62.9 + - - +
161D LEU 4.4 0.2 - - - -
162D ARG* 3.2 9.7 - - - +
163D LEU* 2.8 55.7 + - + +
165D SER* 3.8 24.2 - - - -
169D LEU* 4.4 13.9 - - + -
327D PHE* 3.8 22.0 - - + -
340D VAL* 3.8 19.5 - - + -
345D MET* 5.7 0.9 - - - -
350D VAL* 4.0 11.9 - - + -
351D GLN 3.4 7.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D SER* 3.7 4.6 + - - -
155D LEU* 1.3 81.7 - - - +
157D THR* 1.3 65.8 + - - +
160D GLY 5.8 1.4 + - - -
161D LEU 3.2 6.8 + - - +
162D ARG* 3.5 25.9 - - + +
235D ASP* 2.5 33.2 + - + +
238D LEU* 3.9 20.3 - - + +
241D LEU* 4.0 6.9 - - + +
350D VAL* 3.2 6.6 - - - +
351D GLN* 2.9 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D HIS* 1.3 81.1 - - - +
158D ALA* 1.3 61.1 + - - +
159D SER* 3.2 13.5 + - - -
160D GLY* 2.9 21.3 + - - -
161D LEU* 2.9 35.1 + - + +
163D LEU* 4.1 12.3 - - + -
241D LEU* 3.7 7.2 - - - +
345D MET* 4.0 33.7 - - + -
347D SER* 3.4 15.0 - - - +
349D ALA 3.3 5.2 - - - -
350D VAL* 4.7 3.1 - - + -
----------------------------------------------------------
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