Contacts of the helix formed by residues 137 - 146 (chain X) in PDB entry 1V7M
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 GLY 137 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48X LEU* 4.7 13.0 - - - -
133X HIS* 3.1 17.8 + - - -
134X LEU 3.3 1.8 + - - -
136X ARG* 1.3 76.9 - - - +
138X LYS* 1.3 65.6 + - - -
139X VAL 2.9 3.0 + - - -
140X ARG* 3.0 3.8 + - - -
141X PHE* 3.0 33.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X ASP* 4.3 13.0 + - - -
48X LEU* 4.0 22.0 - - + +
51X TRP* 3.0 73.9 - - + +
62X ASP* 5.4 4.4 - - + +
63X ILE* 3.2 20.9 - - + +
66X ALA* 5.7 5.8 - - + -
117X ARG* 3.5 29.9 - - - +
133X HIS* 4.8 3.3 + - - +
134X LEU* 3.7 23.9 + - + +
137X GLY* 1.3 69.9 - - - -
139X VAL* 1.3 55.5 + - - +
141X PHE* 3.5 0.8 + - - -
142X LEU 3.1 15.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 139 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12X LEU* 3.8 13.7 - - + -
63X ILE* 3.9 30.3 - - + -
100X LEU* 4.4 19.5 - - + -
134X LEU* 3.1 28.4 + - + +
135X LEU* 3.8 12.6 - - + -
137X GLY 2.9 2.4 + - - -
138X LYS* 1.3 73.5 - - - +
140X ARG* 1.3 59.5 + - - +
142X LEU* 3.1 5.1 + - + +
143X MET* 2.9 59.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 140 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216H ARG* 5.1 6.9 + - - +
217H ASP* 2.4 38.6 + - - +
212L GLU* 5.6 5.6 - - - -
12X LEU* 4.5 18.3 - - + +
16X LEU* 4.1 22.0 - - - +
135X LEU 3.8 11.6 + - - +
136X ARG* 3.4 53.2 + - - +
137X GLY 3.0 2.1 + - - +
139X VAL* 1.3 77.5 - - - +
141X PHE* 1.3 66.9 - - + +
143X MET* 3.2 3.5 + - - +
144X LEU* 3.0 48.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 141 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217H ASP* 6.0 1.6 - - - -
211L ASN* 3.2 40.7 + - + -
212L GLU* 4.6 13.2 - - + -
48X LEU* 4.2 25.4 - - + -
51X TRP* 3.9 14.1 - + + -
52X LYS* 4.0 27.6 - - + +
59X LYS* 4.9 4.3 - - - -
136X ARG 4.9 6.3 - - - -
137X GLY* 3.0 23.3 + - - +
138X LYS 3.8 4.9 - - - +
140X ARG* 1.3 89.2 - - + +
142X LEU* 1.3 60.0 + - - +
144X LEU* 4.4 4.3 - - - +
145X VAL* 3.6 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51X TRP* 4.4 3.1 - - + -
56X GLU* 3.7 34.4 - - + +
59X LYS* 3.7 22.4 - - + +
60X ALA* 3.8 22.4 - - + +
63X ILE* 4.1 11.0 - - + -
104X LEU* 5.1 9.9 - - + -
107X LEU* 5.1 9.4 - - + -
138X LYS 3.1 17.1 + - - +
139X VAL* 3.1 5.4 + - + +
141X PHE* 1.3 78.3 - - - +
143X MET* 1.3 71.0 + - + +
144X LEU 3.5 0.4 - - - -
145X VAL* 4.3 1.6 - - - +
146X GLY 3.8 20.6 + - - +
147X GLY* 4.2 7.6 + - - +
150X LEU* 5.3 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 143 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X LEU* 3.4 30.2 - - + +
11X VAL* 4.2 13.0 - - + -
12X LEU* 3.5 36.8 - - + -
15X LEU* 5.9 0.2 - - + -
100X LEU* 5.0 8.1 - - + -
135X LEU* 5.9 0.2 - - + -
139X VAL* 2.9 46.2 + - + +
140X ARG* 4.0 5.2 - - - +
142X LEU* 1.3 82.6 - - + +
144X LEU* 1.3 66.8 + - + +
146X GLY 3.2 17.0 - - - +
147X GLY* 5.9 0.2 - - - -
150X LEU* 3.5 46.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 144 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186L GLU 4.1 4.2 - - - +
210L ARG* 3.3 77.0 + - - +
211L ASN* 4.4 16.8 - - + -
212L GLU* 5.5 1.1 - - - +
9X LEU* 5.1 11.9 - - + -
12X LEU* 5.8 5.4 - - + -
140X ARG* 3.0 35.0 + - + +
141X PHE 4.7 1.1 - - - +
143X MET* 1.3 79.6 - - + +
145X VAL* 1.3 67.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186L GLU 4.6 6.6 - - - +
187L ARG* 5.3 6.2 - - - -
188L HIS 6.0 0.9 - - - -
189L ASN* 5.3 9.9 - - + +
210L ARG* 5.1 2.0 + - - +
211L ASN* 3.6 25.5 - - - +
52X LYS* 3.8 15.7 - - + +
56X GLU* 3.1 33.4 - - + +
59X LYS* 5.7 0.4 - - - -
141X PHE 3.6 19.5 + - - +
142X LEU 4.4 0.7 - - - +
143X MET 3.5 0.6 - - - -
144X LEU* 1.3 82.3 - - - +
146X GLY* 1.3 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 146 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9X LEU* 4.4 8.8 - - - +
56X GLU* 4.6 0.6 + - - -
142X LEU 3.8 7.4 + - - +
143X MET* 3.2 17.5 - - - +
144X LEU 4.7 0.2 - - - -
145X VAL* 1.3 87.6 - - - +
147X GLY* 1.3 65.7 + - - +
150X LEU* 5.1 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