Contacts of the helix formed by residues 102 - 119 (chain A) in PDB entry 4LOX
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 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A THR* 1.3 70.2 - - - +
103A LYS* 1.3 61.9 + - - +
104A LEU 3.0 2.7 - - - -
105A GLY* 3.0 7.9 + - - -
158A ARG* 2.7 55.3 + - - +
159A PRO 5.3 4.1 - - - +
161A ILE* 4.8 9.3 + - - +
164A LYS* 4.1 11.8 + - - +
209A ARG* 3.4 57.1 + - + +
210A ASP* 2.9 13.7 + - - +
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Residues in contact with LYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.5 13.2 - - + +
18A ASP* 3.2 30.3 - - - +
19A ALA 4.9 3.3 + - - -
21A GLY 2.9 22.9 + - - +
22A SER* 4.9 0.2 - - - -
23A PHE* 4.1 25.4 - - + +
99A LEU* 4.7 2.9 - - + -
101A THR* 3.1 11.7 + - - +
102A GLU* 1.3 79.1 - - - +
104A LEU* 1.3 55.9 + - - +
106A ASP* 3.0 19.7 + - + +
107A TYR* 2.9 25.7 + - - +
139A ASN* 5.9 0.4 - - - +
209A ARG* 4.0 11.4 - - - +
15C T 4.1 3.8 + - - -
16C G 2.9 36.1 + - - +
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Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A PHE 5.9 0.2 - - - +
98A SER* 4.7 10.3 - - - +
99A LEU* 3.6 39.8 - - + +
101A THR 3.1 15.1 + - - +
102A GLU 3.0 0.4 - - - -
103A LYS* 1.3 77.9 - - - +
105A GLY* 1.3 57.3 + - - +
107A TYR* 3.2 15.5 + - + +
108A LEU* 2.8 53.0 + - + +
161A ILE* 3.8 24.7 - - + -
164A LYS* 3.6 24.5 - - + -
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Residues in contact with GLY 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLU* 3.0 12.5 + - - -
104A LEU* 1.3 77.0 - - - +
106A ASP* 1.3 61.2 + - - +
108A LEU* 3.3 2.8 + - - +
109A LEU* 3.2 28.0 + - - +
158A ARG* 3.8 15.7 - - - -
159A PRO* 4.0 20.0 - - - +
161A ILE* 3.9 12.4 - - - +
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Residues in contact with ASP 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 4.5 8.1 - - + +
103A LYS* 3.0 25.0 + - + +
105A GLY* 1.3 72.8 - - - +
107A TYR* 1.3 68.4 + - - +
109A LEU* 3.4 5.1 + - - +
110A PHE* 2.9 25.6 + - - +
138A ILE* 3.3 12.0 - - + +
139A ASN* 2.8 44.2 + - - +
158A ARG* 2.7 35.9 + - - +
209A ARG* 4.6 8.5 + - - -
16C G 5.3 1.4 + - - -
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Residues in contact with TYR 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A PHE* 3.7 32.4 - + + -
90A ILE* 4.9 1.1 - - + -
91A LEU* 3.2 44.4 + - + +
94A PHE* 3.6 30.9 - + + +
95A ASP* 2.6 30.6 + - - -
99A LEU* 3.7 23.6 - - + -
103A LYS 2.9 7.5 + - - +
104A LEU* 3.4 15.7 - - + +
106A ASP* 1.3 77.4 - - - +
108A LEU* 1.3 82.1 + - + +
110A PHE* 3.2 9.7 + + - +
111A LYS* 2.8 29.6 + - + +
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Residues in contact with LEU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASP* 5.4 0.9 - - - +
104A LEU* 2.8 40.6 + - + +
105A GLY 3.9 3.8 - - - +
106A ASP 3.1 0.4 - - - -
107A TYR* 1.3 104.8 - - + +
109A LEU* 1.3 63.8 + - - +
111A LYS* 3.4 11.9 + - + +
112A LYS* 3.3 30.6 + - - +
159A PRO* 4.1 26.9 - - + -
161A ILE* 4.5 6.5 - - + -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A GLY 3.2 20.2 + - - +
108A LEU* 1.3 74.3 - - - +
110A PHE* 1.3 65.4 + - - +
112A LYS* 3.1 17.8 + - - +
113A VAL* 3.1 24.8 + - - +
134A LEU* 4.0 17.9 - - + +
137A SER* 3.5 39.5 - - - +
138A ILE* 3.4 21.8 - - + -
156A THR* 3.8 20.2 - - - +
157A PRO 4.6 2.9 - - - +
158A ARG* 4.0 7.6 - - + +
159A PRO* 3.8 28.3 - - + -
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A PHE* 3.6 42.0 - + + -
24A MET 3.5 27.4 - - - -
25A VAL* 4.2 7.4 - - + -
41A ALA* 3.8 13.5 - - + -
42A ILE 3.7 15.0 - - - -
43A PHE* 4.5 0.9 - - + -
86A LEU* 4.2 21.8 - - + -
90A ILE* 4.9 3.6 - - + -
91A LEU* 4.5 6.7 - - + -
106A ASP 2.9 19.1 + - - +
107A TYR* 3.3 11.7 - + - +
109A LEU* 1.3 73.2 - - - +
111A LYS* 1.3 67.7 + - - +
113A VAL* 3.3 7.7 + - - +
114A LEU* 3.2 43.4 + - + +
138A ILE* 4.1 10.2 - - + +
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 3.9 30.4 - - + +
95A ASP* 2.7 42.2 + - - +
107A TYR* 2.8 21.6 + - + +
108A LEU* 3.5 17.5 - - + +
109A LEU 3.2 0.2 - - - -
110A PHE* 1.3 76.2 - - - +
112A LYS* 1.3 64.6 + - + +
114A LEU* 3.2 5.4 + - - +
115A GLU* 3.0 49.4 + - - +
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A LEU* 3.3 18.1 + - - +
109A LEU* 3.1 21.9 + - - +
111A LYS* 1.3 76.6 - - + +
113A VAL* 1.3 66.4 + - - +
115A GLU* 3.1 26.2 + - - +
116A LEU* 3.2 16.8 + - + +
134A LEU* 3.9 28.5 - - + +
156A THR* 5.4 2.4 + - - -
157A PRO 5.8 1.6 + - - -
159A PRO* 5.5 5.0 - - - +
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A VAL* 4.1 30.5 - - + -
39A VAL* 4.6 0.7 - - + -
41A ALA* 4.9 3.4 - - + -
109A LEU 3.1 14.5 + - - +
110A PHE 3.6 7.6 - - - +
111A LYS 3.3 0.2 - - - -
112A LYS* 1.3 75.4 - - - +
114A LEU* 1.3 57.6 + - - +
116A LEU* 2.8 23.9 + - - +
117A MET* 2.9 29.6 + - + +
131A ILE* 4.1 29.8 - - + +
134A LEU* 3.7 29.2 - - + -
135A LYS 5.1 0.2 - - - +
138A ILE* 4.6 2.5 - - + -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ALA* 3.5 24.5 - - + -
83A SER* 4.0 33.2 + - - +
86A LEU* 4.0 12.8 - - + -
87A THR* 3.9 21.1 + - - +
91A LEU* 4.0 20.4 - - + -
110A PHE* 3.2 47.4 + - + +
111A LYS 3.4 8.1 - - - +
113A VAL* 1.3 80.0 - - - +
115A GLU* 1.3 57.0 + - - +
117A MET* 3.7 6.8 - - - +
118A GLY* 2.8 24.9 + - - -
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A LEU* 5.2 5.1 - - + +
111A LYS* 3.0 44.9 + - + +
112A LYS* 3.3 21.9 - - - +
113A VAL 3.0 0.2 - - - -
114A LEU* 1.3 77.7 - - + +
116A LEU* 1.3 67.7 + - + +
118A GLY* 3.2 10.2 + - - -
119A THR* 3.5 15.8 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LYS* 3.2 18.5 + - + +
113A VAL 2.8 7.7 + - - +
115A GLU* 1.3 81.2 - - + +
117A MET* 1.3 60.4 + - - +
119A THR* 3.3 7.0 + - - -
121A GLU* 3.0 59.2 + - + +
122A HIS 4.4 1.6 - - - -
127A GLY 4.9 1.8 - - - +
130A LYS* 4.2 25.8 - - + +
131A ILE* 4.0 21.8 - - + -
134A LEU* 3.8 23.3 - - + -
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Residues in contact with MET 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.4 41.1 - - + +
40A VAL* 4.4 0.7 - - - -
41A ALA* 4.3 14.1 - - - +
83A SER* 3.3 33.8 + - - +
113A VAL* 2.9 26.5 + - + +
114A LEU* 3.7 19.5 - - - +
116A LEU* 1.3 76.5 - - - +
118A GLY* 1.3 64.0 + - - +
120A LYS* 2.9 14.2 + - - +
122A HIS* 3.3 44.3 - - + +
131A ILE* 4.6 0.9 - - + -
5D T 5.8 0.9 - - - +
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Residues in contact with GLY 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR* 5.8 2.2 - - - -
114A LEU 2.8 14.8 + - - -
115A GLU* 3.6 6.7 - - - -
116A LEU 3.2 0.6 - - - -
117A MET* 1.3 78.5 - - - +
119A THR* 1.3 59.1 + - - +
120A LYS* 3.5 11.1 + - - +
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Residues in contact with THR 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLU 3.5 10.1 + - - +
116A LEU 3.3 5.4 + - - -
117A MET 3.2 0.4 - - - -
118A GLY* 1.3 77.3 - - - +
120A LYS* 1.3 71.2 + - - +
121A GLU* 3.0 36.8 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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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