Contacts of the helix formed by residues 120 - 138 (chain A) 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 SER 120 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 1.3 72.3 - - - +
121A GLU* 1.3 54.5 + - - +
122A GLU* 3.1 6.1 - - - -
123A GLU* 2.8 38.0 + - - -
124A ASN* 2.4 42.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU 3.8 0.6 + - - -
120A SER* 1.3 73.2 - - - +
122A GLU* 1.3 56.7 + - - +
124A ASN* 3.8 8.2 - - - +
125A GLU* 3.0 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A SER* 3.1 5.9 - - - -
121A GLU* 1.3 77.3 - - - +
123A GLU* 1.3 61.4 + - + +
125A GLU* 2.9 8.5 + - - +
126A GLN* 2.8 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A GLN 4.9 0.5 - - - +
119A LEU* 3.6 16.4 - - + +
120A SER* 2.8 37.5 + - - +
122A GLU* 1.3 79.4 - - + +
124A ASN* 1.3 56.2 + - - +
126A GLN* 3.3 8.5 + - - +
127A MET* 2.9 30.3 + - - +
130B ASN* 4.2 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU 4.7 0.3 - - - +
116A VAL* 3.3 41.1 + - + +
119A LEU* 2.7 31.1 + - - +
120A SER 2.4 33.5 + - - +
121A GLU* 3.8 7.8 - - - +
123A GLU* 1.3 69.3 - - - +
125A GLU* 1.3 66.9 + - - +
127A MET* 3.4 6.6 - - - +
128A LYS* 2.9 29.1 + - - +
5B TYR* 3.3 17.3 + - - +
134B MET* 4.9 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A GLU 3.0 17.2 + - - +
122A GLU* 2.9 14.0 + - - +
124A ASN* 1.3 74.8 - - - +
126A GLN* 1.3 65.6 + - + +
128A LYS* 4.3 2.4 - - - +
129A ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A GLU* 2.8 26.4 + - - +
123A GLU* 3.6 8.1 - - - +
125A GLU* 1.3 77.0 - - - +
127A MET* 1.3 57.1 + - - +
129A ALA* 3.0 6.9 + - - +
130A ASN* 2.8 51.0 + - - +
123B GLU* 5.6 1.0 - - - +
130B ASN* 6.0 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 6.1 0.9 - - + -
123A GLU 2.9 17.3 + - - +
124A ASN* 3.4 2.9 - - - +
126A GLN* 1.3 75.9 - - - +
128A LYS* 1.3 63.4 + - - +
130A ASN* 3.2 5.2 + - - +
131A LEU* 3.0 30.5 + - + +
5B TYR* 3.2 31.0 - - + +
9B PHE* 4.7 2.9 - - + -
127B MET* 3.8 23.8 - - - +
130B ASN* 3.7 33.8 - - + +
131B LEU* 3.7 25.1 - - + +
134B MET* 3.5 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A ASN 2.9 14.4 + - - +
125A GLU* 4.6 2.5 - - - +
127A MET* 1.3 77.2 - - - +
129A ALA* 1.3 59.4 + - - +
131A LEU* 3.7 2.4 - - - +
132A THR* 2.9 29.3 + - - -
2B GLU* 5.5 6.0 + - - -
3B PHE 4.9 11.9 - - - +
5B TYR* 4.4 15.7 - - + +
8B LEU* 4.0 18.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU 3.1 20.3 + - - +
126A GLN* 3.0 9.3 + - - +
128A LYS* 1.3 76.9 - - - +
130A ASN* 1.3 70.4 + - - +
132A THR* 3.3 15.1 + - - -
133A LYS* 3.4 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A GLN* 2.8 35.9 + - - +
127A MET* 3.8 1.8 - - - +
129A ALA* 1.3 76.0 - - - +
131A LEU* 1.3 58.0 + - - +
133A LYS* 3.1 10.0 + - - +
134A MET* 2.9 31.9 + - - +
119B LEU* 3.2 31.8 - - + +
123B GLU* 3.8 20.5 + - - +
127B MET* 3.7 27.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PHE* 3.8 27.1 - - + -
127A MET* 3.0 24.2 + - + +
128A LYS 3.7 4.9 - - - +
130A ASN* 1.3 76.9 - - - +
132A THR* 1.3 56.3 + - - +
134A MET* 3.2 3.0 + - - -
135A LEU* 2.8 32.0 + - - +
5B TYR* 3.9 18.4 - - + -
8B LEU* 3.8 30.1 - - + -
9B PHE* 3.6 27.4 - - + -
12B ILE* 3.4 16.8 - - + +
127B MET* 3.7 21.8 - - + -
131B LEU* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS 2.9 15.8 + - - -
129A ALA* 3.6 9.1 + - - -
130A ASN 3.2 0.2 - - - -
131A LEU* 1.3 77.6 - - - +
133A LYS* 1.3 53.9 + - - +
135A LEU* 3.3 10.8 + - + +
136A SER* 2.7 35.1 + - - -
2B GLU 4.2 18.1 + - - +
3B PHE* 5.4 5.0 + - + -
8B LEU* 4.5 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A ALA 3.4 7.2 + - - +
130A ASN* 3.1 12.9 + - - +
132A THR* 1.3 80.7 - - - +
134A MET* 1.3 58.7 + - + +
136A SER* 3.1 8.8 + - - -
137A SER* 2.8 30.8 + - - -
118B GLN* 5.0 13.7 - - + +
119B LEU* 5.5 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A TYR* 3.0 45.8 - - + -
9A PHE* 4.2 8.5 - - + -
130A ASN 2.9 17.8 + - - +
131A LEU* 3.7 4.5 - - - +
133A LYS* 1.3 75.0 - - - +
135A LEU* 1.3 62.4 + - - +
137A SER* 2.6 22.2 + - - -
138A LEU* 3.3 15.1 - - - +
12B ILE* 4.0 11.0 - - + -
115B LEU* 3.5 46.8 - - + +
116B VAL* 5.3 0.2 - - - -
118B GLN* 4.7 4.5 - - + -
119B LEU* 4.2 19.1 - - + -
127B MET* 3.6 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A LEU 2.8 18.3 + - - +
132A THR* 3.4 10.3 - - + +
134A MET* 1.3 74.7 - - - +
136A SER* 1.3 66.9 + - - +
138A LEU* 2.9 19.0 + - + +
139A GLN 3.4 18.2 - - - +
7B TYR* 5.4 9.2 - - + +
8B LEU* 4.9 10.8 - - + -
11B MET* 3.5 21.8 - - + +
12B ILE* 3.4 45.6 - - + +
15B GLU* 4.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A THR* 2.7 19.6 + - - -
133A LYS* 3.3 12.3 - - - -
135A LEU* 1.3 76.2 - - - +
137A SER* 1.3 53.5 + - - +
139A GLN* 2.7 33.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 137 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A LYS 2.8 14.1 + - - -
134A MET* 2.6 29.6 + - - -
136A SER* 1.3 71.6 - - - +
138A LEU* 1.3 61.2 + - - +
139A GLN 3.2 2.9 + - - -
19B LYS* 5.6 1.0 - - - +
114B THR* 5.5 5.8 - - - +
115B LEU* 3.9 8.1 - - - +
118B GLN* 3.2 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A MET 3.3 14.1 - - - +
135A LEU* 2.9 9.3 + - - +
137A SER* 1.3 87.6 - - - +
139A GLN* 1.3 70.5 + - - +
12B ILE* 4.0 18.6 - - + +
15B GLU* 4.2 24.5 - - + +
16B MET* 3.4 41.7 - - + +
19B LYS* 4.4 27.3 - - + +
111B MET* 5.9 3.4 - - + +
114B THR* 5.9 5.6 - - + -
115B LEU* 4.1 17.3 - - + -
----------------------------------------------------------
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