Contacts of the strand formed by residues 17 - 31 (chain A) in PDB entry 5J0Z
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 THR 17 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 1.3 92.3 - - - +
18A VAL* 1.3 58.0 + - - +
19A ASN* 3.1 27.0 + - - +
46A SER 4.2 0.7 - - - +
47A TRP* 4.0 8.1 - - - +
48A LYS 4.8 0.3 + - - -
141A VAL* 3.4 21.2 - - - +
143A ALA* 4.3 14.4 - - + +
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Residues in contact with VAL 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 4.0 9.6 - - + +
17A THR* 1.3 76.7 - - - +
19A ASN* 1.3 63.7 + - - +
20A THR* 3.5 4.4 + - - +
45A LEU* 4.5 9.0 - - + -
46A SER 3.7 15.3 - - - +
47A TRP* 4.3 8.3 - - + -
74A PRO* 3.9 31.0 - - + -
76A ILE* 4.4 9.4 - - + -
140A ILE* 3.4 32.1 - - + -
141A VAL 2.8 11.5 + - - +
142A LEU* 3.4 11.9 - - + -
143A ALA 2.9 25.3 + - - +
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Residues in contact with ASN 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 3.1 33.7 + - - +
18A VAL* 1.3 70.2 + - - +
20A THR* 1.3 60.9 + - - +
44A SER* 3.3 8.5 + - - +
45A LEU* 3.4 1.5 - - - -
46A SER* 2.7 49.8 + - - +
143A ALA* 3.5 11.2 + - - +
144A VAL 4.5 2.5 - - - +
145A ASP* 4.0 31.4 + - + +
148A LYS* 5.0 1.4 - - - -
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Residues in contact with THR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL 3.7 13.2 - - - +
19A ASN* 1.3 71.5 - - - +
21A GLY* 1.3 58.4 + - - +
44A SER* 3.3 7.0 - - - -
45A LEU* 3.8 20.6 - - + -
76A ILE* 5.1 0.9 - - + -
130A LEU* 4.1 15.7 - - + -
142A LEU* 4.0 20.2 - - + -
143A ALA 2.8 18.6 + - - +
144A VAL* 3.6 1.0 - - - +
145A ASP* 2.8 29.8 + - - +
184A LEU* 3.0 17.6 - - + +
186A TYR* 2.8 19.9 + - - -
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Residues in contact with GLY 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A THR* 1.3 76.3 - - - +
22A ILE* 1.3 62.4 + - - -
23A TYR 4.1 0.2 + - - -
42A PHE 3.5 1.2 - - - +
43A LEU* 3.5 4.1 - - - +
44A SER* 2.8 47.5 + - - -
148A LYS* 3.2 21.7 - - - +
149A VAL* 3.9 6.7 - - - -
186A TYR* 3.6 4.7 - - - -
177B GLU* 4.9 0.3 - - - +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY* 1.3 76.6 - - - +
23A TYR* 1.3 62.4 + - - +
24A LEU* 4.0 14.8 - - + -
41A ALA* 3.9 18.4 - - + -
42A PHE 3.2 7.9 - - - +
43A LEU* 4.0 14.1 - - + -
78A PHE* 4.0 20.9 - - + -
106A PHE* 4.2 7.6 - - + -
128A ILE* 4.1 11.4 - - + -
130A LEU* 3.9 12.1 - - + -
148A LYS 3.4 2.8 + - - -
149A VAL* 3.6 3.7 - - - +
150A GLY 3.4 11.6 + - - -
165A PHE* 3.3 19.5 - - + -
186A TYR* 3.7 47.4 - - + -
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Residues in contact with TYR 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A GLY 4.1 0.6 + - - -
22A ILE* 1.3 72.3 - - - +
24A LEU* 1.3 65.0 + - - +
25A ILE* 3.5 11.4 + - + +
41A ALA* 3.3 3.0 - - - -
42A PHE* 2.9 45.0 + + + -
148A LYS 5.9 0.2 - - - -
149A VAL 4.7 0.7 - - - -
150A GLY* 3.3 23.3 - - - +
151A LYS 3.3 30.5 + - - -
152A ASN* 2.7 30.7 + - - -
176B LEU* 3.6 38.8 - - + +
177B GLU* 3.5 24.7 - - + +
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Residues in contact with LEU 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 ILE* 4.0 4.7 - - + -
23A TYR* 1.3 75.4 - - - +
25A ILE* 1.3 60.2 + - - +
26A GLU 4.8 0.7 - - - +
27A CYS* 3.9 27.8 - - - -
39A VAL* 3.4 29.4 - - + -
41A ALA* 3.7 11.7 - - + -
128A ILE* 4.4 4.7 - - + -
150A GLY 3.2 5.6 + - - +
151A LYS* 3.4 14.6 - - + -
152A ASN 3.0 24.3 + - - -
155A VAL* 3.9 2.8 - - + +
165A PHE* 3.6 53.6 - - + -
188A LEU* 4.2 12.1 - - + -
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Residues in contact with ILE 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 3.6 19.3 - - + +
24A LEU* 1.3 75.4 - - - +
26A GLU* 1.3 69.2 + - + +
40A ASN* 2.7 10.9 + - - +
41A ALA* 3.7 4.7 - - - -
42A PHE* 3.6 38.4 - - + +
105A ARG* 3.4 47.6 - - + +
152A ASN* 4.2 15.8 + - - +
154A ASP* 5.1 2.1 - - - +
155A VAL* 3.4 13.8 + - - +
79B VAL* 4.0 23.9 - - + +
176B LEU* 6.1 0.9 - - + -
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Residues in contact with GLU 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 LEU* 3.7 0.4 - - - -
25A ILE* 1.3 91.8 + - + +
27A CYS* 1.3 63.5 + - - +
28A TYR* 3.8 14.3 - - + -
39A VAL* 3.4 7.0 - - - +
40A ASN* 2.8 54.6 + - + +
154A ASP* 5.5 4.5 - - - +
155A VAL* 4.0 7.4 - - - +
156A PHE* 5.6 2.1 - - - -
79B VAL* 3.9 11.8 - - - +
80B ASN* 3.1 42.3 - - - +
81B VAL 3.3 7.0 + - - +
111B LEU* 4.1 23.5 - - + +
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Residues in contact with CYS 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LEU* 3.9 18.6 - - - -
26A GLU* 1.3 78.4 - - - +
28A TYR* 1.3 64.2 + - - +
37A PHE* 5.0 4.5 - - + -
38A LYS 3.5 7.0 - - - +
39A VAL* 4.5 4.7 - - + +
155A VAL* 3.6 28.5 - - + +
156A PHE 3.2 22.2 + - - +
157A LEU* 3.8 20.0 - - + -
162A ILE* 5.2 2.5 - - - -
188A LEU* 3.8 31.4 - - + -
111B LEU* 5.3 2.9 - - - +
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Residues in contact with TYR 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 GLU* 3.8 24.2 - - + -
27A CYS* 1.3 79.8 - - - +
29A SER* 1.3 73.8 + - - +
30A LEU 3.5 2.8 + - - -
37A PHE* 3.8 1.7 - - - +
38A LYS* 2.8 74.6 + - + +
39A VAL 4.4 6.4 + - - -
40A ASN* 4.3 9.3 - - + +
107A SER* 4.5 6.2 - - - -
156A PHE 5.1 1.8 - - - +
157A LEU* 3.7 9.1 - - - +
82B GLU* 3.2 65.8 + - + +
111B LEU* 3.5 22.0 - - + -
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Residues in contact with SER 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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28A TYR* 1.3 86.7 - - - +
30A LEU* 1.3 62.1 + - - +
31A ASP* 2.9 14.8 + - - +
36A THR* 3.6 1.9 + - - +
37A PHE* 3.3 13.3 - - - -
38A LYS* 3.8 18.7 + - - +
157A LEU* 4.4 1.4 - - - +
82B GLU* 4.8 2.1 + - - -
109B ARG* 5.7 0.3 + - - -
402B SO4 3.0 31.1 + - - -
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Residues in contact with LEU 30 (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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28A TYR 3.5 2.6 - - - -
29A SER* 1.3 74.1 - - - +
31A ASP* 1.3 59.5 + - - +
32A ASP* 3.6 17.2 + - - +
36A THR 3.4 10.8 - - - +
37A PHE* 3.9 5.2 - - + -
114A LEU* 3.7 28.9 - - + -
126A LEU* 4.2 18.4 - - + -
157A LEU* 3.9 19.9 - - + +
158A THR 5.8 0.9 - - - +
160A TRP* 3.7 34.3 + - + +
190A ILE* 3.3 34.3 - - + -
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Residues in contact with ASP 31 (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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29A SER* 2.9 7.9 + - - +
30A LEU* 1.3 72.5 - - - +
32A ASP* 1.3 53.5 + - - +
33A LYS* 3.2 12.7 + - - +
34A ALA* 3.1 28.4 + - + +
35A GLU* 2.7 32.2 + - - -
36A THR* 2.9 28.6 + - - +
109A ARG* 4.3 6.0 + - - +
406A SO4 4.7 3.3 + - - -
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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