Contacts of the helix formed by residues 122 - 139 (chain J) in PDB entry 4LLL
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 GLU 122 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J GLU* 1.3 71.2 - - - +
123J GLU* 1.3 53.6 + - - +
124J ASN* 3.2 6.5 - - - +
125J GLU* 2.6 42.7 + - + +
126J GLN* 3.4 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119J LEU* 3.3 14.5 - - + -
120J SER* 2.9 25.1 + - - -
121J GLU* 2.6 29.0 + - + +
122J GLU* 1.3 79.1 - - - +
124J ASN* 1.3 67.1 + - - +
126J GLN* 3.0 27.8 + - - +
127J MET* 3.8 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 124 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I TYR* 3.4 26.2 + - - +
116J VAL* 3.4 28.3 + - - +
119J LEU* 2.9 39.4 + - + -
120J SER 4.8 1.2 + - - -
121J GLU 3.2 10.3 + - - +
122J GLU* 3.7 2.4 - - - +
123J GLU* 1.3 77.9 - - - +
125J GLU* 1.3 95.4 + - - +
126J GLN 3.0 1.8 - - - -
127J MET* 3.2 17.2 + - - +
128J LYS* 3.3 9.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J GLU* 2.6 31.2 + - + +
124J ASN* 1.3 88.9 + - - +
126J GLN* 1.3 60.7 + - - +
128J LYS* 3.3 15.7 + - - +
129J ALA* 3.4 10.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122J GLU 3.4 2.1 + - - +
123J GLU* 3.0 15.6 + - - +
125J GLU* 1.3 80.2 - - - +
127J MET* 1.3 57.1 + - - +
129J ALA* 2.9 11.9 + - - +
130J ASN* 2.8 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I TYR* 4.7 17.5 - - + +
127I MET* 3.1 53.2 - - + +
130I ASN* 3.1 37.0 - - + -
131I LEU* 3.6 10.8 - - - +
123J GLU 3.8 1.8 + - - +
124J ASN* 3.2 14.9 + - - +
126J GLN* 1.3 78.2 - - - +
128J LYS* 1.3 54.8 + - - +
130J ASN* 2.8 7.6 + - - -
131J LEU* 2.6 36.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I PHE 4.9 20.2 - - - +
5I TYR* 4.8 16.7 - - + -
8I LEU* 6.1 0.2 - - - +
124J ASN 3.3 8.0 + - - +
125J GLU* 3.3 13.6 + - - +
126J GLN 3.1 0.4 - - - -
127J MET* 1.3 79.6 - - - +
129J ALA* 1.3 56.2 + - - +
131J LEU* 3.5 5.8 + - - +
132J THR* 2.7 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125J GLU 3.4 5.2 + - - +
126J GLN* 2.9 14.4 + - - +
128J LYS* 1.3 81.0 - - - +
130J ASN* 1.3 63.1 + - - +
132J THR* 3.0 22.4 + - - -
133J LYS* 3.2 8.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 130 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119I LEU* 4.6 11.1 - - + +
123I GLU* 4.6 20.0 - - + -
127I MET* 3.9 20.3 - - + +
126J GLN 2.8 12.2 + - - +
127J MET* 2.8 15.0 + - - +
129J ALA* 1.3 77.1 - - - +
131J LEU* 1.3 63.0 + - - +
132J THR 3.3 0.2 + - - -
133J LYS* 3.3 8.1 + - - +
134J MET* 3.2 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I LEU* 4.9 18.6 - - + +
127I MET* 4.5 9.8 - - + -
9J PHE* 5.7 9.6 - - + -
127J MET* 2.6 20.5 + - + +
128J LYS* 3.9 6.3 - - - +
130J ASN* 1.3 72.9 - - - +
132J THR* 1.3 52.6 + - - +
134J MET* 2.7 29.9 + - - +
135J LEU* 2.7 19.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J LYS 2.7 18.3 + - - -
129J ALA* 3.1 13.0 - - - -
131J LEU* 1.3 79.4 - - - +
133J LYS* 1.3 63.5 + - - +
135J LEU* 3.2 9.5 + - - +
136J SER* 3.1 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118I GLN* 3.6 22.9 - - - +
119I LEU* 4.8 4.9 - - + -
129J ALA 3.2 7.0 + - - +
130J ASN* 3.7 7.6 - - - +
131J LEU 3.2 0.2 - - - -
132J THR* 1.3 80.5 - - - +
134J MET* 1.3 63.8 + - - +
136J SER* 2.9 22.9 + - - -
137J SER* 3.3 7.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ILE* 6.5 1.3 - - + -
115I LEU* 5.8 9.2 - - + +
118I GLN* 4.5 9.9 - - + -
119I LEU* 6.2 1.1 - - + -
127I MET* 5.4 7.0 - - + -
9J PHE* 5.7 9.9 - - + -
130J ASN 3.2 9.8 + - - +
131J LEU* 2.7 16.6 + - - +
133J LYS* 1.3 80.5 - - - +
135J LEU* 1.3 61.8 + - - +
137J SER* 2.8 26.2 + - - -
138J LEU* 3.8 2.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I TYR* 5.3 7.4 - - + -
8I LEU* 4.7 13.0 - - + +
11I MET* 4.1 26.7 - - + -
12I ILE* 4.6 18.6 - - + +
15I GLU* 6.0 5.2 - - + -
131J LEU 2.7 14.5 + - - +
132J THR* 3.6 12.6 - - - +
133J LYS 3.2 0.2 - - - -
134J MET* 1.3 68.3 - - - +
136J SER* 1.3 71.7 + - - +
137J SER 2.7 3.1 + - - -
138J LEU* 3.0 7.5 + - + +
139J GLN* 3.0 39.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132J THR 3.1 8.3 + - - -
133J LYS* 2.9 18.0 + - - -
135J LEU* 1.3 85.5 - - - +
137J SER* 1.3 66.1 + - - +
139J GLN* 3.5 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114I THR* 4.9 13.0 + - - +
115I LEU* 6.5 0.2 - - - -
118I GLN* 3.4 27.2 - - - +
133J LYS 3.3 3.3 + - - -
134J MET* 2.8 16.0 + - - -
135J LEU 2.7 1.2 + - - -
136J SER* 1.3 83.0 - - - +
138J LEU* 1.3 59.4 + - - +
139J GLN 5.0 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ILE 5.7 0.7 - - - +
15I GLU* 3.6 39.0 - - + +
16I MET* 4.7 8.3 - - + +
19I LYS* 5.4 9.1 - - + +
134J MET 3.8 2.0 + - - +
135J LEU* 3.0 7.7 + - + +
137J SER* 1.3 80.2 - - - +
139J GLN* 1.3 68.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 139 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I GLU* 4.4 17.9 - - + +
58J GLN* 5.6 5.8 + - + +
135J LEU* 3.0 37.9 + - + +
136J SER* 3.5 11.9 + - - +
137J SER 5.0 0.4 - - - -
138J LEU* 1.3 84.0 - - - +
----------------------------------------------------------
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