Contacts of the helix formed by residues 110 - 131 (chain B) in PDB entry 4LXZ
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 110 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 3.3 21.5 - - - -
108B PHE 3.4 0.8 + - - -
109B ASP* 1.3 73.1 - - - +
111B LEU* 1.3 65.5 + - - +
112B PHE 3.3 2.9 - - - -
113B GLU* 3.1 11.9 + - - -
114B PHE 2.9 19.9 + - - -
407B PG4 4.7 5.1 - - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.5 10.8 - - + +
84B ILE* 4.0 31.4 - - + +
101B VAL* 4.8 3.6 - - + -
106B PRO 4.0 9.4 - - - +
107B VAL* 4.4 7.4 - - + -
108B PHE* 3.2 41.1 + - + +
109B ASP 3.3 1.0 + - - -
110B GLY* 1.3 76.4 - - - +
112B PHE* 1.3 64.5 + - - +
114B PHE* 3.2 2.6 + - - +
115B CYS* 3.0 30.6 + - - -
157B TYR* 3.6 57.2 - - + -
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Residues in contact with PHE 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA 5.0 1.1 - - - -
66B ALA 5.1 1.8 - - - -
69B MET* 3.8 33.9 - - + -
78B ILE* 4.1 19.1 - - + -
81B LEU* 3.5 38.8 + - + +
82B ARG* 3.6 51.6 - - + +
110B GLY 3.3 0.8 - - - -
111B LEU* 1.3 79.0 - - - +
113B GLU* 1.3 52.0 + - - +
115B CYS* 3.1 11.5 + - + +
116B GLN* 2.8 73.4 + - + +
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B TYR* 2.5 32.1 + - + +
63B LYS* 3.3 33.8 + - + -
110B GLY* 3.1 14.6 + - - +
112B PHE* 1.3 77.5 - - - +
114B PHE* 1.3 63.2 + - - +
116B GLN* 3.2 11.2 + - - +
117B LEU* 2.9 30.0 + - - +
404B NHE 3.4 20.7 - - + +
407B PG4 3.6 19.3 - - - +
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Residues in contact with PHE 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 3.7 28.0 - - + -
27B TYR* 3.7 36.4 - + + -
29B TYR* 3.5 24.0 - + - -
35B MET* 5.8 3.4 - - + -
37B PRO* 3.7 26.9 - - + -
108B PHE* 4.2 17.7 - + + -
110B GLY 2.9 12.0 + - - +
111B LEU* 3.4 9.9 - - + +
113B GLU* 1.3 75.1 - - - +
115B CYS* 1.3 66.0 + - - +
117B LEU* 3.9 1.0 - - - +
118B SER* 2.9 36.3 + - - -
141B ALA* 4.9 5.2 - - + -
144B LEU* 4.1 23.8 - - + -
157B TYR* 5.2 2.2 - + - -
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Residues in contact with CYS 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B MET* 4.1 5.6 - - + -
81B LEU* 4.8 3.8 - - - -
111B LEU* 3.0 30.7 + - - -
112B PHE* 3.3 12.8 - - + +
114B PHE* 1.3 79.0 - - - +
116B GLN* 1.3 58.2 + - - +
118B SER* 2.7 22.7 + - - -
119B THR* 2.9 21.8 + - - -
144B LEU* 6.5 1.1 - - - -
157B TYR* 3.5 35.4 - - - -
158B VAL* 3.8 24.5 - - + -
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Residues in contact with GLN 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B HIS 3.6 0.3 - - - +
63B LYS* 3.2 42.6 + - + +
64B ALA* 3.0 43.2 + - - +
65B THR* 4.8 3.2 - - - +
69B MET* 3.7 10.8 - - + -
82B ARG* 4.6 8.7 - - - +
112B PHE* 2.8 49.1 + - + +
113B GLU* 3.2 17.6 + - - +
115B CYS* 1.3 74.4 - - - +
117B LEU* 1.3 53.0 + - - +
120B GLY* 2.8 28.8 + - - -
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ASP* 3.8 32.3 - - + +
24B ILE* 3.8 17.3 - - + +
27B TYR* 3.7 35.9 - - + +
61B PRO* 3.8 28.8 - - + +
62B HIS 4.3 3.4 - - - +
63B LYS* 3.8 23.6 - - + -
113B GLU 2.9 16.6 + - - +
114B PHE 3.9 0.2 - - - +
116B GLN* 1.3 73.0 - - - +
118B SER* 1.3 66.6 + - - +
120B GLY 3.5 0.2 + - - -
121B GLY* 3.3 18.7 + - - -
139B ASN* 4.8 1.9 + - - +
141B ALA* 5.0 1.7 - - - +
404B NHE 3.7 17.0 - - + -
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ILE* 4.4 1.0 - - - +
114B PHE* 2.9 21.9 + - - -
115B CYS* 2.7 26.7 + - - -
117B LEU* 1.3 77.4 - - - +
119B THR* 1.3 61.2 + - - -
122B SER* 3.7 3.8 + - - -
139B ASN* 2.9 26.3 + - - -
141B ALA* 3.2 35.0 - - - -
142B GLY* 4.2 1.5 - - - -
144B LEU* 4.5 16.1 - - - +
158B VAL* 5.4 1.7 + - - +
160B ASP* 4.0 5.9 - - - +
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA* 3.6 21.1 - - + -
68B GLU* 5.7 0.7 - - + -
69B MET* 4.4 4.5 - - + +
115B CYS 2.9 19.1 + - - -
118B SER* 1.3 73.7 + - - +
120B GLY* 1.3 65.0 + - - +
122B SER* 3.2 3.6 + - - -
123B VAL* 3.0 32.3 + - + +
158B VAL* 3.3 24.2 + - + +
160B ASP* 3.6 18.7 + - - +
163B LEU* 3.6 27.8 - - + -
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Residues in contact with GLY 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PRO* 3.9 6.1 - - - -
62B HIS* 3.5 30.3 - - - -
64B ALA* 3.8 4.5 - - - +
116B GLN 2.8 22.5 + - - -
117B LEU 3.9 0.4 - - - -
118B SER 3.4 0.2 - - - -
119B THR* 1.3 73.7 - - - +
121B GLY* 1.3 56.0 + - - +
123B VAL* 5.0 0.2 - - - -
124B ALA* 2.9 34.7 + - - +
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Residues in contact with GLY 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B TYR* 3.7 22.3 - - - -
61B PRO* 3.5 14.8 - - - +
117B LEU 3.3 11.1 + - - -
118B SER 3.6 0.2 + - - -
119B THR 3.3 0.4 - - - -
120B GLY* 1.3 75.3 - - - +
122B SER* 1.3 57.2 + - - +
125B GLY* 3.0 25.1 + - - -
139B ASN* 3.5 23.4 - - - +
301B LEU* 5.1 0.5 - - - +
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B THR 3.2 7.0 + - - -
121B GLY* 1.3 72.9 - - - +
123B VAL* 1.3 64.0 + - - +
125B GLY* 3.4 1.2 + - - -
126B ALA* 3.1 23.7 + - - +
139B ASN* 2.9 17.7 + - - +
160B ASP* 2.7 46.7 + - - +
164B ALA* 3.7 11.5 - - - +
301B LEU* 3.9 4.5 - - - +
303B LEU* 3.3 18.9 - - - +
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B HIS* 4.9 2.2 - - + -
68B GLU* 3.6 31.9 - - + +
119B THR* 3.0 27.5 + - + +
120B GLY 4.3 1.6 - - - +
122B SER* 1.3 74.9 - - - +
124B ALA* 1.3 59.4 + - - +
126B ALA* 3.2 7.9 + - - +
127B VAL* 2.9 38.7 + - + +
160B ASP 4.9 1.1 - - - +
163B LEU* 3.9 35.4 - - + +
164B ALA* 4.3 2.2 - - - +
167B GLU* 4.7 12.6 - - + +
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Residues in contact with ALA 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 3.5 33.7 + - + +
61B PRO* 5.5 1.3 - - + -
62B HIS* 4.2 16.3 - - + +
120B GLY 2.9 19.7 + - - +
121B GLY 4.1 0.4 - - - +
123B VAL* 1.3 78.6 - - - +
125B GLY* 1.3 57.2 + - - +
127B VAL* 3.2 9.8 + - - +
128B LYS* 3.0 23.9 + - - +
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Residues in contact with GLY 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B TYR* 3.7 13.4 - - - -
121B GLY 3.0 16.6 + - - -
122B SER 3.8 1.6 - - - -
123B VAL 3.3 0.2 - - - -
124B ALA* 1.3 72.1 - - - +
126B ALA* 1.3 59.1 + - - +
128B LYS* 3.3 4.9 + - - +
129B LEU* 3.0 33.9 + - - +
137B ALA* 3.6 23.2 - - - +
301B LEU* 4.3 4.0 - - - -
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B SER 3.1 14.1 + - - +
123B VAL 3.5 8.7 - - - +
125B GLY* 1.3 71.5 - - - +
127B VAL* 1.4 59.9 + - - +
129B LEU* 3.4 7.4 + - - +
130B ASN* 3.0 32.4 + - - -
164B ALA* 3.5 28.9 - - + +
167B GLU* 3.6 14.4 - - + -
168B LEU* 3.7 16.4 - - + +
301B LEU* 4.4 4.7 - - + +
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Residues in contact with VAL 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B VAL* 2.9 26.7 + - + +
124B ALA* 3.2 10.9 + - - +
126B ALA* 1.4 76.0 - - - +
128B LYS* 1.4 62.4 + - + +
130B ASN* 3.1 4.5 + - + +
131B ARG* 3.0 61.3 + - + +
133B GLN* 5.9 0.2 - - - +
167B GLU* 3.5 31.4 - - - +
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B CYS* 4.1 20.1 - - - -
19B TYR* 3.3 23.6 - - + +
59B TYR* 3.0 31.2 + - - -
124B ALA 3.0 8.5 + - - +
125B GLY* 3.3 11.0 + - - +
127B VAL* 1.4 74.9 - - + +
129B LEU* 1.3 61.2 + - - +
131B ARG 3.5 1.2 + - - -
132B GLN 3.2 3.3 + - - -
133B GLN* 2.9 71.1 + - + +
134B THR* 3.7 14.5 + - + -
137B ALA* 5.2 0.9 - - + -
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Residues in contact with LEU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B GLY 3.0 20.6 + - - +
126B ALA* 3.6 9.4 - - - +
128B LYS* 1.3 76.2 - - - +
130B ASN* 1.3 57.8 + - - +
132B GLN* 3.0 22.7 + - - +
134B THR* 3.6 19.4 - - + +
135B ASP 3.4 34.3 - - - +
136B MET* 4.0 0.9 - - - +
137B ALA* 4.2 3.8 - - + -
168B LEU* 4.2 15.3 - - + -
172B HIS* 4.9 6.1 + - - +
262B VAL 5.4 0.2 - - - +
299B PRO* 3.9 19.6 - - + +
300B LEU* 3.7 22.0 - - - +
301B LEU* 3.7 30.5 - - + +
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Residues in contact with ASN 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B ALA 3.0 11.1 + - - -
127B VAL* 3.5 9.6 - - + +
129B LEU* 1.3 75.7 - - - +
131B ARG* 1.3 60.2 + - + +
132B GLN* 3.3 15.2 + - - +
167B GLU* 2.8 52.3 + - - +
168B LEU* 3.5 9.0 - - - +
171B TYR* 3.4 46.9 - - + +
172B HIS* 3.4 30.0 - - - -
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B VAL* 3.0 41.0 + - + +
128B LYS 4.1 0.7 - - - +
129B LEU 3.3 0.2 - - - -
130B ASN* 1.3 76.0 - - + +
132B GLN* 1.4 69.1 + - - +
133B GLN* 3.1 36.3 + - - +
171B TYR* 5.2 10.2 + - + +
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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) + - + + + + + -
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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