Contacts of the strand formed by residues 140 - 150 (chain H) in PDB entry 1VPO
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 MET 140 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H THR* 5.6 0.5 - - - -
138H ASN* 3.0 37.4 + - - +
139H SER* 1.3 92.3 - - - +
141H VAL* 1.3 63.2 + - - +
187H THR* 3.4 29.6 - - + +
188H VAL* 3.4 28.0 - - - -
189H PRO* 3.7 21.8 - - + -
190H SER* 4.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PRO* 3.7 28.9 - - + -
140H MET* 1.3 76.6 - - - +
142H THR* 1.3 67.7 + - - +
143H LEU* 4.1 6.2 + - + -
186H VAL 3.9 0.5 - - - +
187H THR* 3.2 2.6 - - - -
188H VAL* 2.8 56.0 + - + +
189H PRO 4.3 0.2 - - - +
190H SER* 3.7 22.2 - - - -
193H TRP* 4.4 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 142 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PRO* 3.8 6.1 - - - +
141H VAL* 1.3 76.0 - - - +
143H LEU* 1.3 78.1 + - - +
185H SER* 4.3 13.9 - - - -
186H VAL 3.4 7.4 - - - +
187H THR* 3.0 22.6 + - - +
119L THR* 5.3 6.9 - - - +
121L SER* 3.8 24.1 + - - +
123L PHE* 3.1 26.0 - - + -
140L PHE* 4.3 4.5 - - + -
142L ASN* 4.6 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 143 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H LEU 3.6 6.3 - - - +
131H PRO* 3.5 31.6 - - + -
141H VAL* 4.4 6.7 - - + +
142H THR* 1.3 78.1 - - - +
144H GLY* 1.3 59.5 + - - +
185H SER* 3.3 8.5 - - - -
186H VAL* 2.7 39.3 + - + +
188H VAL* 4.7 6.1 - - + -
193H TRP* 3.6 43.1 - - + +
198H VAL* 3.5 37.0 - - + -
215H ILE* 3.9 14.4 - - + -
123L PHE* 4.1 4.7 - - - -
140L PHE* 4.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 144 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H LEU* 2.8 44.5 + - - +
143H LEU* 1.3 79.6 - - - +
145H CYS* 1.3 59.3 + - - -
159H TRP* 3.4 8.4 - - - -
184H SER 3.1 12.3 - - - -
185H SER* 4.1 0.9 - - - -
215H ILE* 3.2 14.0 - - - +
140L PHE* 4.1 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 145 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H VAL* 4.6 3.8 - - + -
127H TYR 3.4 9.2 - - - -
128H PRO* 4.5 2.0 - - - -
129H LEU* 3.6 4.7 - - - +
144H GLY* 1.3 79.0 - - - -
146H LEU* 1.3 61.1 + - - +
147H VAL* 4.6 6.7 - - + +
157H VAL* 5.3 1.6 - - + -
159H TRP* 3.6 8.5 - - + -
183H SER* 3.2 6.9 - - - -
184H SER* 2.9 33.3 + - - +
200H CYS* 2.0 51.8 - - + -
213H LYS* 4.5 3.1 - - - -
215H ILE* 3.6 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 146 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H SER 3.4 1.4 - - - +
126H VAL* 3.3 4.5 - - - +
127H TYR* 2.7 65.9 + - + +
129H LEU* 4.2 14.5 - - + +
145H CYS* 1.3 72.8 - - - +
147H VAL* 1.3 64.4 + - - +
148H LYS* 3.9 9.2 - - + -
181H THR* 3.6 30.3 - - + -
182H LEU 3.7 4.9 - - - +
183H SER* 4.4 9.4 - - - +
129L GLN* 4.7 1.6 - - - +
136L SER* 3.6 33.4 - - - +
138L VAL* 4.2 12.8 - - + -
183L THR* 4.6 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 147 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H PRO* 3.5 28.9 - - + -
125H SER 3.2 4.3 - - - +
126H VAL* 4.5 4.9 - - + -
145H CYS* 4.6 7.4 - - + +
146H LEU* 1.3 78.4 - - - +
148H LYS* 1.3 59.5 + - - +
150H TYR* 3.8 14.5 - - + -
155H VAL* 4.3 5.8 - - + -
157H VAL* 4.5 11.9 - - + -
181H THR* 3.3 2.1 - - - -
182H LEU* 2.7 50.9 + - + +
184H SER* 6.4 0.2 - - - -
202H VAL* 3.8 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 148 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H SER* 2.9 36.6 + - - -
127H TYR* 4.0 19.5 - - + +
146H LEU* 3.9 8.3 - - + -
147H VAL* 1.3 75.8 - - - +
149H GLY* 1.3 65.5 + - - +
150H TYR* 3.4 2.9 - - - -
176H GLN* 4.5 7.5 + - - -
180H TYR 3.5 4.0 - - - -
181H THR* 3.1 29.6 - - + +
129L GLN* 4.0 19.8 - - - +
136L SER* 3.8 5.2 + - - +
183L THR* 6.1 0.9 - - + +
185L THR* 3.2 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 149 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H THR* 3.2 18.4 - - - +
123H PRO 3.1 13.5 - - - +
148H LYS* 1.3 82.3 - - - +
150H TYR* 1.3 59.7 + - - +
179H LEU* 3.8 28.2 - - - +
180H TYR 2.9 10.5 + - - -
181H THR* 4.0 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 150 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122H THR 3.0 12.3 - - - +
123H PRO 3.9 0.4 - - - -
124H PRO* 3.3 24.2 - - + -
147H VAL* 3.8 33.0 - - + -
148H LYS 3.4 0.4 - - - -
149H GLY* 1.3 80.0 - - - +
151H PHE* 1.3 67.1 + - - +
152H PRO 3.5 17.3 - - - -
153H GLU* 2.6 27.6 + - - -
155H VAL* 3.2 30.5 - - + +
173H ALA* 3.0 18.2 - - - +
179H LEU* 3.7 0.5 - - - -
180H TYR* 2.9 57.9 + + + +
181H THR 4.2 1.1 - - - -
182H LEU* 3.9 12.6 - - + +
204H HIS* 3.9 2.2 - - + -
----------------------------------------------------------
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