Contacts of the helix formed by residues 151 - 164 (chain B) in PDB entry 2LL6
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 VAL 151 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLU* 4.4 33.2 - - + +
14A GLU* 5.4 9.0 - - + +
15A ALA* 4.7 12.1 - - + +
149B LEU* 6.1 0.2 - - - -
150B LYS* 1.3 93.1 - - + +
152B LEU* 1.3 63.1 + - + +
153B VAL 3.0 8.2 + - - -
154B LYS* 3.2 20.5 + - - +
155B ALA* 3.7 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A PHE* 3.5 27.1 - - + -
105A LEU* 6.0 2.2 - - + -
108A VAL* 4.6 13.7 - - + -
109A MET* 4.9 20.6 - - + -
112A LEU* 5.3 13.9 - - + -
124A MET* 6.3 2.9 - - + -
149B LEU* 4.5 12.6 - - + -
150B LYS 4.4 1.0 - - - +
151B VAL* 1.3 83.0 - - + +
153B VAL* 1.3 58.7 + - - +
154B LYS 3.4 0.2 - - - -
155B ALA* 3.8 11.3 + - + +
156B VAL* 3.1 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA* 5.2 1.4 - - - +
92A PHE* 4.7 2.7 - - - -
141A PHE* 3.4 39.7 - - + +
144A MET* 4.9 8.1 - - + +
145A MET* 4.7 19.3 - - + +
149B LEU* 3.5 28.3 - - + +
150B LYS* 3.5 31.4 - - - +
151B VAL 3.0 0.6 - - - -
152B LEU* 1.3 78.3 - - - +
154B LYS* 1.3 62.6 + - + +
156B VAL* 3.8 6.6 + - - +
157B LEU* 3.6 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 6.0 1.0 - - - +
8A GLN* 4.4 21.9 + - - +
11A GLU* 4.6 35.4 - - + +
12A PHE* 5.2 4.3 - - + +
15A ALA* 4.9 11.2 - - + -
72A MET* 5.0 21.4 - - + +
76A MET* 5.7 7.3 - - - +
145A MET* 4.3 20.8 + - + +
150B LYS 3.9 16.8 - - - +
151B VAL* 3.2 9.7 + - - +
153B VAL* 1.3 78.5 - - + +
155B ALA* 1.3 60.8 + - - +
157B LEU* 3.6 11.0 + - + +
158B PHE* 3.0 40.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA* 5.5 5.3 - - + +
18A LEU* 5.7 6.5 - - + -
19A PHE* 3.6 42.1 - - + -
35A VAL* 5.6 0.5 - - - +
151B VAL 3.7 8.0 + - - +
152B LEU* 4.0 15.5 - - + +
153B VAL 3.4 0.6 - - - -
154B LYS* 1.3 78.4 - - - +
156B VAL* 1.3 61.9 + - + +
158B PHE* 3.7 3.6 + - - +
159B ALA* 3.6 16.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 5.3 2.9 - - + -
88A ALA* 3.9 19.1 - - + +
91A VAL* 3.7 42.2 - - + -
92A PHE* 3.6 22.2 - - + -
108A VAL* 6.4 0.7 - - + -
152B LEU* 3.1 27.4 - - + +
153B VAL 3.8 5.1 + - - +
154B LYS 3.4 0.4 - - - -
155B ALA* 1.3 75.0 - - + +
157B LEU* 1.3 63.0 + - - +
158B PHE 3.3 0.7 - - - -
159B ALA* 3.5 5.6 + - + +
160B CYS* 2.9 33.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET* 6.5 0.4 - - + -
76A MET* 4.5 11.2 - - + -
84A GLU* 4.3 35.0 - - + +
85A ILE* 4.9 7.2 - - + +
88A ALA* 5.0 9.9 - - + -
141A PHE* 5.9 0.7 - - + -
145A MET* 3.4 37.2 - - + -
153B VAL* 3.6 22.3 + - + +
154B LYS* 3.6 13.4 + - + +
155B ALA 3.4 0.4 - - - -
156B VAL* 1.3 77.6 - - - +
158B PHE* 1.3 62.7 + - + +
160B CYS* 3.7 6.3 + - + +
161B MET* 3.1 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 5.2 4.5 - - + -
68A PHE* 3.0 79.4 - + + -
71A MET* 4.3 18.3 - - + +
72A MET* 3.4 46.0 - - + -
154B LYS* 3.0 29.8 + - + -
155B ALA* 4.0 9.0 - - - +
156B VAL 3.3 0.4 - - - -
157B LEU* 1.3 80.1 - - + +
159B ALA* 1.3 62.8 + - - +
161B MET* 3.5 9.1 + - + +
162B LEU* 3.1 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 5.5 3.1 - - + -
32A LEU* 5.8 3.4 - - + -
35A VAL* 4.5 20.9 - - + -
36A MET* 4.2 13.9 - - + +
39A LEU* 5.2 14.1 - - + -
155B ALA 3.6 10.5 + - - +
156B VAL* 3.5 8.6 + - - +
158B PHE* 1.3 78.6 - - - +
160B CYS* 1.3 61.0 + - - +
162B LEU* 4.0 7.0 - - - +
163B MET* 3.1 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU* 6.0 2.2 - - - -
84A GLU* 4.9 3.6 - - + +
87A GLU* 3.3 62.5 - - + +
88A ALA 4.4 0.9 - - - -
90A ARG* 5.8 0.7 - - - -
91A VAL* 4.5 5.6 - - - -
156B VAL* 2.9 32.5 + - - +
157B LEU* 4.0 7.9 - - + +
158B PHE 3.3 0.2 - - - -
159B ALA* 1.3 78.0 - - - +
161B MET* 1.3 60.6 + - + +
163B MET* 4.1 2.9 - - - +
164B ARG* 3.4 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET* 4.4 26.9 - - + +
72A MET* 4.4 25.4 - - + +
75A LYS* 4.5 17.5 - - - +
84A GLU* 2.9 33.4 - - + +
157B LEU* 3.1 37.0 + - + +
158B PHE* 3.5 15.6 + - + +
159B ALA 3.3 0.2 - - - -
160B CYS* 1.3 77.4 - - + +
162B LEU* 1.3 62.1 + - - +
163B MET 3.4 0.4 - - - -
164B ARG* 4.2 3.5 - - - +
165B LYS* 3.6 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.1 24.5 - - + -
36A MET* 5.1 1.1 - - + -
51A MET* 3.1 70.9 - - + +
54A GLU* 4.7 4.5 - - + -
55A VAL* 4.8 3.4 - - + -
63A ILE* 5.0 9.4 - - + -
68A PHE* 5.6 3.4 - - + -
71A MET* 3.5 34.3 - - + -
158B PHE* 3.1 32.8 + - + +
159B ALA* 3.7 4.0 + - - +
161B MET* 1.3 76.7 - - - +
163B MET* 1.3 60.3 + - - +
165B LYS* 4.0 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A MET* 3.8 26.9 - - + -
41A GLN* 3.5 34.1 - - + +
47A GLU* 5.8 0.7 - - - +
51A MET* 3.9 11.0 - - + +
87A GLU* 5.7 4.9 - - - +
90A ARG* 6.3 1.6 - - - +
159B ALA 3.1 20.2 + - - +
160B CYS* 4.5 4.3 - - - +
162B LEU* 1.3 76.2 - - - +
164B ARG* 1.3 59.9 + - + +
165B LYS* 3.1 12.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 4.1 34.0 + - - +
84A GLU* 5.9 2.6 - - - +
87A GLU* 5.0 19.4 - - - +
160B CYS 3.4 19.1 + - - +
161B MET* 4.2 4.0 + - - +
162B LEU 3.6 0.2 - - - -
163B MET* 1.3 79.8 - - + +
165B LYS* 1.3 60.8 + - - +
----------------------------------------------------------
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