Contacts of the strand formed by residues 135 - 145 (chain R) in PDB entry 4M8B
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 LEU 135 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56R GLU* 4.1 9.0 - - - +
124R LYS* 4.3 23.3 - - + +
125R PHE* 4.1 13.9 - - - +
126R ASN* 3.7 25.1 - - + +
133R THR* 3.5 20.4 + - - +
134R LYS* 1.3 85.9 - - - +
136R GLU* 1.3 64.9 + - - +
137R THR* 4.7 1.9 + - - -
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Residues in contact with GLU 136 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R ASN* 2.8 28.8 + - - +
56R GLU* 3.5 19.9 - - + +
57R LYS* 4.3 17.6 + - - +
123R LEU 3.7 0.9 - - - +
124R LYS* 3.3 4.3 - - - +
125R PHE 3.0 36.3 + - - +
127R MET* 3.7 30.9 - - + +
134R LYS* 4.2 16.8 + - + +
135R LEU* 1.3 77.8 - - - +
137R THR* 1.3 62.0 + - - +
138R PHE* 4.1 9.6 - - + -
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Residues in contact with THR 137 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54R ASN* 3.6 3.5 - - - +
55R GLU* 2.8 60.6 + - - +
56R GLU* 3.0 16.6 + - - -
122R SER* 4.7 10.5 - - - -
123R LEU 3.5 6.3 - - - +
124R LYS* 3.4 34.4 + - + +
135R LEU 4.7 2.1 + - - -
136R GLU* 1.3 75.2 + - - +
138R PHE* 1.3 65.8 + - - +
139R HIS* 3.6 12.3 - - + +
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Residues in contact with PHE 138 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R PHE* 3.8 22.0 - + + -
24R VAL* 5.0 8.1 - - + -
25R PHE* 3.5 40.6 - + - -
31R CYS* 6.4 0.9 - - + -
52R VAL* 4.6 11.9 - - + -
53R PHE 3.6 2.9 - - - +
54R ASN* 3.7 38.8 - - + -
121R PHE 3.8 0.7 - - - +
122R SER* 3.4 4.7 - - - -
123R LEU* 2.8 48.7 + - + +
125R PHE* 4.3 11.2 - - + -
127R MET* 3.9 19.5 - - + -
136R GLU* 4.1 21.1 - - + -
137R THR* 1.3 74.3 - - - +
139R HIS* 1.3 62.5 + - - +
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Residues in contact with HIS 139 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A T 6.2 0.2 - - - -
11A G 5.6 0.2 - - - -
21R PHE* 5.0 0.4 - - - -
51R PHE 3.6 0.3 - - - +
52R VAL* 3.1 10.3 - - - +
53R PHE* 2.9 68.0 + + + -
55R GLU* 2.8 42.7 + - + +
60R ILE 4.0 0.4 + - - -
61R LYS 3.3 27.6 - - - -
122R SER* 5.3 2.0 - - - -
137R THR* 3.6 11.7 - - + +
138R PHE* 1.3 77.1 - - - +
140R LEU* 1.3 60.2 + - - +
141R ILE 4.3 0.4 - - - -
301R EDO 2.6 37.5 + - - +
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Residues in contact with LEU 140 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R ILE* 4.4 10.8 - - + -
17R LEU* 3.4 29.2 - - + -
20R VAL* 4.1 20.4 - - + -
21R PHE* 4.0 17.7 - - + -
50R ILE* 4.3 7.6 - - + -
51R PHE 3.3 7.2 - - - +
52R VAL* 4.0 16.4 - - + -
78R PHE* 5.3 2.5 - - + -
119R LYS* 4.7 2.7 - - + +
120R THR* 3.1 7.5 - - - -
121R PHE* 2.8 45.7 + - + +
139R HIS* 1.3 75.4 - - - +
141R ILE* 1.3 78.3 + - - +
142R ALA* 4.3 12.8 - - + +
301R EDO 3.9 0.4 + - - -
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Residues in contact with ILE 141 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A T 4.3 1.6 - - - +
49R ASN 3.9 0.5 - - - +
50R ILE* 3.3 4.2 - - - +
51R PHE* 2.7 49.3 + - + +
53R PHE* 4.2 10.1 - - + -
63R TRP* 3.7 42.8 - - + +
118R LYS* 3.6 28.9 - - + -
119R LYS 3.7 1.3 - - - -
120R THR* 3.4 22.7 - - + -
140R LEU* 1.3 79.7 - - - +
142R ALA* 1.3 63.3 + - - +
143R TYR* 3.8 14.8 - - + -
301R EDO 3.8 20.9 - - - +
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Residues in contact with ALA 142 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9R GLY 5.7 1.6 - - - +
10R TYR* 6.0 0.9 - - + -
11R ILE* 4.3 17.5 - - + +
49R ASN 3.5 4.0 - - - -
50R ILE* 4.0 17.9 - - + -
118R LYS* 3.3 5.0 - - - -
119R LYS* 3.0 51.7 + - + +
140R LEU* 4.3 3.1 - - + -
141R ILE* 1.3 77.7 - - - +
143R TYR* 1.3 65.3 + - - +
144R TYR* 3.8 4.8 - - + -
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Residues in contact with TYR 143 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9R GLY 4.7 2.3 - - - +
44R LEU* 3.8 15.6 - - + +
45R VAL* 3.2 37.7 - - + +
46R ASN 3.6 16.8 - - - +
47R PRO* 4.1 0.2 - - - -
48R GLY* 2.8 26.4 + - - -
49R ASN* 2.9 15.5 + - + +
51R PHE* 3.8 21.3 - + - -
63R TRP* 2.7 24.3 + - - -
65R ASP* 2.6 29.6 + - + +
69R TRP* 3.8 12.1 - + - -
116R LEU* 4.7 2.5 - - + -
117R LEU 3.4 12.6 - - - +
118R LYS* 3.9 10.5 - - + -
141R ILE* 3.8 18.6 - - + +
142R ALA* 1.3 75.9 - - - +
144R TYR* 1.3 65.9 + - - +
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Residues in contact with TYR 144 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R TYR* 3.6 32.7 + + + -
47R PRO* 4.2 11.2 - - - +
80R VAL* 4.1 18.4 - - - +
116R LEU* 3.4 8.8 - - - +
117R LEU* 2.7 72.8 + - + +
118R LYS 4.3 0.2 - - - -
119R LYS* 3.5 48.3 + - + +
142R ALA* 3.8 7.0 - - + -
143R TYR* 1.3 81.2 - - - +
145R THR* 1.3 60.5 + - - +
148R ASP* 5.3 0.2 - - + -
149R ILE* 3.9 16.8 - - + -
154R LEU* 3.9 17.5 - - + -
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Residues in contact with THR 145 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47R PRO* 4.4 14.8 - - + -
115R GLY* 3.0 22.1 + - - -
116R LEU* 4.1 3.1 + - - -
117R LEU* 4.4 0.9 - - - +
144R TYR* 1.3 85.0 - - - +
146R GLU* 1.3 69.9 + - - +
147R LYS* 3.6 14.2 + - + +
148R ASP* 2.9 53.1 + - - +
149R ILE* 3.3 11.1 + - - +
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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