Contacts of the strand formed by residues 21 - 30 (chain A) in PDB entry 4LML
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 ILE 21 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A GLY* 1.3 79.4 - - - +
22A TYR* 1.3 62.9 + - - +
23A LEU* 4.1 5.2 - - + -
40A ALA* 3.8 19.1 - - + -
41A PHE 3.0 8.5 - - - +
42A LEU* 4.0 10.5 - - + -
77A PHE* 4.3 10.8 - - + -
105A PHE* 4.1 6.7 - - + -
127A ILE* 4.1 17.3 - - + -
129A LEU* 3.9 26.7 - - + -
146A GLU 3.1 12.6 + - - +
147A LYS* 3.5 10.5 - - - +
149A GLY 3.8 2.1 - - - +
164A PHE* 3.6 26.3 - - + -
185A TYR* 3.8 31.0 + - + -
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Residues in contact with TYR 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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21A ILE* 1.3 73.5 - - - +
23A LEU* 1.3 72.1 + - - +
24A ILE* 3.3 7.8 + - + +
40A ALA* 3.1 4.6 - - - +
41A PHE* 2.9 49.9 + + + +
146A GLU 4.2 4.3 - - - +
149A GLY* 3.4 20.9 - - - -
150A LYS 3.1 32.8 + - - -
151A ASN* 3.6 22.1 + - - -
173C PHE* 6.1 1.0 - - - -
175C LEU* 3.6 48.6 - - + +
176C GLU* 3.9 14.8 + - + +
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Residues in contact with LEU 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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21A ILE* 4.0 8.2 - - + -
22A TYR* 1.3 74.5 - - - +
24A ILE* 1.3 56.9 + - - +
26A CYS* 4.1 16.2 - - - -
38A VAL* 3.6 27.1 - - + -
39A ASN 4.4 0.2 - - - -
40A ALA* 3.8 2.9 - - - -
127A ILE* 5.0 3.4 - - + -
149A GLY 3.6 5.9 + - - -
150A LYS* 3.3 18.4 - - + -
151A ASN 2.7 32.4 + - - -
154A VAL* 4.1 9.0 - - + -
161A ILE* 5.8 0.9 - - + -
164A PHE* 3.6 57.2 - - + -
187A LEU* 3.8 18.2 - - + -
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Residues in contact with ILE 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 TYR* 3.3 16.4 + - + +
23A LEU* 1.3 77.2 - - - +
25A GLU* 1.3 75.5 + - + +
39A ASN 2.9 10.8 + - - +
40A ALA* 4.1 18.4 - - - -
41A PHE* 4.2 19.5 - - + -
104A ARG* 3.5 46.2 - - - +
151A ASN* 3.9 25.0 - - - +
153A ASP* 4.8 0.5 - - - +
154A VAL* 3.1 17.6 + - - +
76C ARG* 5.1 1.6 - - - +
78C VAL* 4.0 19.3 - - + +
175C LEU* 6.0 0.2 - - + -
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Residues in contact with GLU 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 ILE* 1.3 87.8 - - + +
26A CYS* 1.3 72.0 + - - +
27A TYR* 3.8 20.8 - - + -
37A LYS 3.8 0.2 - - - +
38A VAL* 3.4 5.5 - - - +
39A ASN* 2.8 45.9 + - + +
153A ASP* 4.4 15.0 - - - +
154A VAL* 4.3 0.2 - - - -
155A PHE* 4.3 12.0 + - - +
78C VAL* 4.0 22.3 - - - +
79C ASN* 3.8 26.0 - - - +
80C VAL 4.3 7.6 - - - +
110C LEU* 4.1 17.2 - - + +
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Residues in contact with CYS 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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23A LEU* 4.1 19.7 - - - -
25A GLU* 1.3 82.8 + - - +
27A TYR* 1.3 67.7 - - - +
36A PHE* 5.3 3.1 - - - -
37A LYS 3.5 4.9 - - - +
38A VAL* 4.3 13.5 - - - -
154A VAL* 4.2 14.6 - - + +
155A PHE* 3.7 7.7 + - - +
156A LEU* 2.9 40.8 + - + +
161A ILE* 4.8 3.1 - - + -
187A LEU* 3.8 27.6 - - - -
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Residues in contact with TYR 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 GLU* 3.8 23.8 - - + -
26A CYS* 1.3 80.9 - - - +
28A SER* 1.3 79.3 + - - +
29A LEU 3.3 2.8 + - - -
37A LYS* 2.9 61.1 + - + +
38A VAL 4.7 3.3 + - - -
39A ASN* 4.3 7.8 - - + +
106A SER* 5.0 0.3 - - - -
107A ALA 5.6 0.2 + - - -
155A PHE* 5.6 0.4 - - + -
156A LEU* 3.8 15.7 - - - +
157A THR* 5.0 4.7 - - + +
33C ALA 5.9 1.3 - - - +
81C GLU* 2.4 71.3 + - + +
82C ASN* 4.0 7.8 + - - -
110C LEU* 3.4 28.0 - - + -
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Residues in contact with SER 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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27A TYR* 1.3 89.5 - - - +
29A LEU* 1.3 65.8 + - - +
30A ASP* 3.3 6.9 + - - +
35A THR* 3.5 1.2 + - - +
36A PHE* 3.5 12.6 - - - -
37A LYS* 3.6 33.9 + - - +
108A ARG* 5.5 1.7 + - - -
156A LEU* 4.4 0.6 - - - +
157A THR* 5.1 8.0 + - - -
33C ALA* 5.7 4.9 - - - +
81C GLU* 4.0 5.9 + - - -
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Residues in contact with LEU 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 TYR 3.3 2.2 - - - -
28A SER* 1.3 75.1 - - - +
30A ASP* 1.3 63.6 + - - +
31A ASP* 3.7 22.2 + - - +
35A THR 3.6 4.7 - - - +
36A PHE* 4.0 9.4 - - + -
113A LEU* 4.3 11.7 - - + -
125A LEU* 4.1 18.8 - - + -
156A LEU* 3.5 23.4 - - + +
157A THR 5.6 1.6 + - - +
159A TRP* 3.5 40.4 + - + +
189A ILE* 3.6 30.3 - - + -
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Residues in contact with ASP 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 SER 3.3 4.4 + - - +
29A LEU* 1.3 72.7 - - - +
31A ASP* 1.3 54.7 + - - +
32A LYS* 3.2 21.4 + - - +
33A ALA* 3.2 25.4 + - + +
34A GLU* 2.8 30.8 + - - -
35A THR* 2.7 22.0 + - - +
108A ARG* 4.6 5.8 + - - +
113A LEU* 4.2 1.6 - - - +
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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