Contacts of the strand formed by residues 21 - 30 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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176B GLU* 4.8 0.2 - - - -
20C GLY* 1.3 79.1 - - - +
22C TYR* 1.3 61.4 + - - +
23C LEU* 3.5 29.2 - - + -
40C ALA* 3.7 9.6 - - + -
41C PHE 3.2 9.2 - - - +
42C LEU* 3.9 13.9 - - + -
77C PHE* 4.7 0.2 - - + -
105C PHE* 4.6 11.4 - - + -
127C ILE* 4.4 12.8 - - + -
129C LEU* 4.1 20.9 - - + -
146C GLU 2.8 20.9 + - - +
147C LYS* 3.8 4.9 - - - +
149C GLY* 3.3 11.6 + - - -
164C PHE* 3.9 14.4 - - + -
185C TYR* 3.8 33.0 - - + -
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Residues in contact with TYR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B PHE* 6.1 0.7 - - - -
175B LEU* 3.3 46.9 - - + +
176B GLU* 3.6 21.0 + - + +
21C ILE* 1.3 73.5 - - - +
23C LEU* 1.3 78.2 + - - +
24C ILE* 3.3 15.4 + - + +
40C ALA* 3.2 2.8 - - - +
41C PHE* 2.9 45.8 + + + +
146C GLU 4.5 0.9 - - - +
148C VAL* 5.3 7.2 - - + -
149C GLY* 3.3 16.6 - - - -
150C LYS 2.8 28.5 + - - -
151C ASN* 3.7 22.2 + - - -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 3.5 23.6 - - + -
22C TYR* 1.3 79.2 - - - +
24C ILE* 1.3 60.8 + - - +
26C CYS* 4.2 10.5 - - - -
38C VAL* 3.8 24.0 - - + -
39C ASN 4.3 0.9 - - - +
40C ALA* 3.8 2.7 - - + -
127C ILE* 5.3 3.1 - - + -
149C GLY 3.3 17.4 + - - +
150C LYS* 3.3 25.8 - - + -
151C ASN 3.3 6.6 + - - -
154C VAL* 4.5 9.0 - - + -
164C PHE* 3.5 40.2 - - + -
187C LEU* 3.9 26.0 - - + -
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Residues in contact with ILE 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 5.0 0.4 - - - +
78B VAL* 4.1 23.1 - - + +
130B ILE* 6.1 2.0 - - + -
22C TYR* 3.6 20.6 - - + +
23C LEU* 1.3 73.5 - - - +
25C GLU* 1.3 71.6 - - + +
39C ASN 2.9 9.8 + - - +
40C ALA* 3.6 24.5 - - - -
41C PHE* 3.7 21.1 - - + +
104C ARG* 3.3 54.1 - - + +
151C ASN* 4.1 15.6 + - - +
153C ASP* 5.3 0.7 - - - +
154C VAL* 3.4 17.2 + - - +
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Residues in contact with GLU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B VAL* 3.9 21.9 - - - +
79B ASN* 3.5 26.4 + - - +
80B VAL 4.1 11.0 - - - +
110B LEU* 3.5 23.8 - - + +
23C LEU* 5.3 0.2 - - - +
24C ILE* 1.3 87.0 + - + +
26C CYS* 1.3 71.0 + - - +
27C TYR* 3.9 12.6 - - + -
38C VAL* 3.8 1.2 - - - +
39C ASN* 2.9 47.9 + - + +
153C ASP* 5.3 7.9 - - - +
154C VAL* 4.5 3.3 - - - -
155C PHE* 4.9 7.4 + - - +
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Residues in contact with CYS 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 4.5 0.5 - - - +
23C LEU* 4.2 17.7 - - - -
25C GLU* 1.3 82.3 + - - +
27C TYR* 1.3 67.7 + - - +
36C PHE* 5.2 3.8 - - + -
37C LYS 3.7 6.5 - - - +
38C VAL* 4.4 13.2 - - - -
154C VAL* 4.5 16.8 - - + +
155C PHE* 4.1 8.0 + - - +
156C LEU* 3.3 35.6 + - + +
161C ILE* 5.0 4.5 - - + -
187C LEU* 3.7 29.6 - - + -
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Residues in contact with TYR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B GLU* 2.5 71.2 + - + +
82B ASN* 4.3 6.5 + - - -
110B LEU* 3.7 23.6 - - + -
25C GLU* 3.9 18.6 - - + -
26C CYS* 1.3 84.2 - - - +
28C SER* 1.3 72.3 + - - +
29C LEU 3.4 2.3 + - - -
36C PHE* 4.3 1.2 - - - +
37C LYS* 2.9 65.6 + - + +
38C VAL 4.4 4.5 + - - -
39C ASN* 4.0 13.4 - - + +
106C SER* 4.5 1.7 - - - -
107C ALA 5.2 0.7 + - - -
156C LEU* 4.1 14.4 - - - +
157C THR 5.4 0.7 - - - +
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Residues in contact with SER 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA* 5.9 2.6 - - - +
81B GLU* 4.4 5.5 + - - -
27C TYR* 1.3 85.4 - - - +
29C LEU* 1.3 63.9 + - - +
30C ASP* 3.3 7.2 + - - +
35C THR* 3.6 1.6 + - - +
36C PHE* 3.4 11.6 - - - -
37C LYS* 3.6 33.4 + - - +
108C ARG* 5.1 1.2 + - - -
156C LEU* 4.5 1.0 - - - +
157C THR* 5.5 4.8 + - - +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TYR 3.4 2.4 + - - -
28C SER* 1.3 74.5 - - - +
30C ASP* 1.3 62.3 - - - +
31C ASP* 3.7 11.5 + - - +
35C THR 3.5 5.6 - - - +
36C PHE* 3.8 9.6 - - + -
113C LEU* 4.2 22.9 - - + -
125C LEU* 3.5 36.3 - - + -
156C LEU* 3.7 20.4 - - + +
159C TRP* 3.8 32.7 + - + +
189C ILE* 3.6 19.1 - - + -
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Residues in contact with ASP 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C SER 3.3 3.9 + - - +
29C LEU* 1.3 72.5 - - - +
31C ASP* 1.3 56.9 + - - +
32C LYS* 3.2 11.2 + - - +
33C ALA* 3.2 33.2 + - + +
34C GLU* 2.7 35.0 + - - -
35C THR* 2.6 20.6 + - - +
108C ARG* 4.4 6.8 + - - +
113C LEU* 4.2 1.4 - - - +
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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