Contacts of the strand formed by residues 21 - 29 (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 GLY 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ILE* 2.8 32.2 + - - +
20A GLU* 1.3 79.8 - - - +
22A SER* 1.3 64.3 + - - -
44A SER 3.3 11.2 - - - -
45A VAL* 4.3 4.9 - - - -
103A LYS* 2.9 29.3 + - - -
15C T 4.2 0.9 - - - +
16C G 3.2 0.3 + - - -
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Residues in contact with SER 22 (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* 5.1 0.2 - - - +
20A GLU 4.7 0.5 + - - -
21A GLY* 1.3 72.4 + - - -
23A PHE* 1.3 65.5 + - - +
24A MET* 3.8 27.8 - - - -
42A ILE 3.6 1.0 - - - +
43A PHE* 3.6 8.0 - - - -
44A SER* 2.9 35.1 + - - +
103A LYS* 4.8 0.7 - - - +
139A ASN* 5.0 0.9 - - - -
15C T 3.2 20.1 - - - +
16C G 2.7 29.3 + - - -
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Residues in contact with PHE 23 (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* 3.9 18.6 - - + -
22A SER* 1.3 73.3 - - - +
24A MET* 1.3 59.8 + - - +
42A ILE 3.7 2.9 - - - -
43A PHE* 3.4 36.8 - + - -
90A ILE* 4.6 2.2 - - + -
94A PHE* 3.9 14.8 - + - -
99A LEU* 3.6 29.4 - - + -
103A LYS* 4.1 21.7 - - + +
106A ASP* 4.4 4.5 - - + +
107A TYR* 3.7 28.5 - + + +
110A PHE* 3.6 46.4 - + + -
138A ILE* 3.6 11.5 - - - +
139A ASN* 2.9 20.5 + - - +
16C G 4.9 0.2 + - - -
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Residues in contact with MET 24 (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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22A SER* 3.8 13.7 - - - -
23A PHE* 1.3 78.3 - - - +
25A VAL* 1.3 72.1 + - - +
26A ARG* 5.7 2.5 - - + -
41A ALA* 3.5 0.7 - - - -
42A ILE* 2.8 54.2 + - + +
44A SER* 3.3 36.3 - - - +
79A ARG* 3.9 15.5 - - - +
110A PHE* 3.5 3.0 - - - -
138A ILE* 5.0 0.2 - - - -
139A ASN* 4.0 4.7 - - - +
16C G 3.6 31.2 - - + -
17C G 3.6 28.7 - - - +
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Residues in contact with VAL 25 (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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24A MET* 1.3 81.1 - - - +
26A ARG* 1.3 65.3 + - - +
27A VAL* 4.1 15.9 - - + -
39A VAL* 4.8 1.3 - - + -
40A VAL 3.2 9.9 - - - +
41A ALA* 4.6 2.5 - - + -
110A PHE* 4.2 13.7 - - + -
113A VAL* 4.1 32.3 - - + -
131A ILE* 4.3 7.2 - - + -
135A LYS* 2.6 46.5 + - + +
138A ILE* 4.0 30.1 - - + +
17C G 4.9 1.9 + - - -
18C A 5.3 0.2 + - - -
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Residues in contact with ARG 26 (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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24A MET* 5.7 3.1 - - + -
25A VAL* 1.3 75.8 - - - +
27A VAL* 1.3 64.7 + - - +
28A ARG* 3.5 36.8 - - + +
38A LEU 4.1 0.7 - - - -
39A VAL* 3.5 0.7 - - - -
40A VAL* 2.7 47.0 + - + +
42A ILE* 3.9 22.2 - - + -
135A LYS* 4.6 1.6 - - - +
17C G 6.1 2.5 - - + -
18C A 3.2 58.1 + - + +
19C G 2.7 55.3 + - - -
6D C 4.9 2.6 - - - +
7D C 4.7 1.8 - - - +
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Residues in contact with VAL 27 (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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25A VAL* 4.1 17.6 + - + -
26A ARG* 1.3 77.2 - - - +
28A ARG* 1.2 63.2 + - - +
29A LYS 3.8 1.0 + - - -
37A TRP* 3.9 27.7 - - + -
38A LEU 3.2 4.3 - - - +
39A VAL* 4.4 7.2 - - + -
128A LEU* 4.0 22.2 - - + -
131A ILE* 4.1 18.6 - - + -
132A VAL* 4.4 8.3 - - + -
135A LYS* 4.1 15.3 - - + +
145A GLU* 5.4 2.1 - - - +
146A LEU* 4.1 28.5 - - + +
18C A 5.7 0.2 + - - -
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Residues in contact with ARG 28 (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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26A ARG* 3.5 48.4 - - + +
27A VAL* 1.2 76.5 - - - +
29A LYS* 1.3 68.5 + - - +
30A ASN* 5.5 3.2 - - + +
37A TRP* 3.1 4.8 - - - -
38A LEU* 2.6 66.7 + - + +
40A VAL* 4.8 4.6 - - - +
145A GLU* 5.8 0.2 - - - -
19C G 3.3 29.2 + - - +
20C G 2.8 52.1 + - - -
21C A 4.7 1.9 - - - +
5D T 4.5 6.9 + - - -
6D C 4.2 4.6 - - - +
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Residues in contact with LYS 29 (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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27A VAL 3.8 0.2 + - - -
28A ARG* 1.3 72.8 - - - +
30A ASN* 1.3 67.0 + - - +
31A SER 5.3 1.3 - - - +
36A GLY 3.6 5.8 - - - +
37A TRP* 3.3 44.2 - - + -
145A GLU* 2.9 43.2 + - - +
149A ALA* 5.4 3.2 - - - +
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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
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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