Contacts of the strand formed by residues 120 - 127 (chain A) in PDB entry 5L4Q
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 TRP 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A PHE* 3.3 5.5 - - - +
78A VAL* 2.7 52.0 + - + +
79A ASN* 5.3 1.6 - - - -
80A ASN 5.8 1.1 - - - -
84A LEU* 4.3 24.7 - - + +
111A ILE* 3.8 32.3 - - + -
112A ASN 3.4 8.1 - - - +
113A ASN* 3.2 53.4 - - + +
117A GLY 4.6 0.8 + - - -
118A ASP* 3.2 27.6 + - - +
119A VAL* 1.3 76.5 - - - +
121A GLU* 1.3 60.3 + - - +
122A VAL 3.9 0.3 + - - -
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Residues in contact with GLU 121 (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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39A PHE* 3.7 13.3 - - - -
75A ARG* 3.2 38.6 + - + -
76A MET 3.7 2.9 - - - +
77A PHE* 3.8 17.7 - - + -
110A SER 3.6 2.1 - - - +
111A ILE* 3.4 2.9 - - - -
112A ASN* 2.7 44.4 + - + +
114A VAL* 3.5 21.4 - - + +
120A TRP* 1.3 72.3 - - - +
122A VAL* 1.3 61.2 + - - +
123A LEU* 4.0 23.2 + - + +
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Residues in contact with VAL 122 (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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74A LYS 3.6 0.9 - - - +
75A ARG* 3.3 7.4 - - - +
76A MET* 2.9 48.6 + - + +
78A VAL* 4.3 17.3 - - + -
84A LEU* 4.8 0.9 - - + -
87A CYS* 3.8 39.0 - - + -
91A ILE* 4.0 23.1 - - + -
110A SER 3.5 4.5 - - - +
111A ILE* 4.3 14.8 - - + -
120A TRP 4.6 0.2 - - - +
121A GLU* 1.3 74.0 - - - +
123A LEU* 1.3 63.9 + - - +
124A ILE* 4.3 11.4 - - + -
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Residues in contact with LEU 123 (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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39A PHE* 4.2 20.2 - - + -
40A GLY 3.5 25.4 - - - +
41A ILE* 3.9 17.3 - - + -
73A LEU* 4.2 9.9 - - + -
74A LYS 3.4 2.7 - - - +
75A ARG* 3.4 41.7 - - + -
109A SER* 3.0 8.1 - - - -
110A SER* 2.9 48.3 + - - +
112A ASN* 5.5 2.0 - - - +
121A GLU* 4.0 22.0 - - + +
122A VAL* 1.3 72.8 - - - +
124A ILE* 1.3 64.0 + - - +
125A LEU 4.2 0.2 - - - -
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Residues in contact with ILE 124 (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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72A ALA 3.6 1.0 - - - +
73A LEU* 3.5 5.6 - - - +
74A LYS* 2.9 46.2 + - + +
76A MET* 4.4 10.3 - - + -
90A GLU* 3.9 34.5 - - + +
91A ILE* 3.7 28.3 - - + -
94A MET* 3.8 18.2 - - - -
106A TYR* 4.2 13.5 - - + -
108A ASP 3.7 7.4 - - - +
109A SER* 4.4 0.2 - - - -
122A VAL* 4.3 8.1 - - + -
123A LEU* 1.3 79.7 - - - +
125A LEU* 1.3 61.8 + - - +
126A MET* 3.7 21.2 + - + +
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Residues in contact with LEU 125 (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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41A ILE* 4.3 13.0 - - + +
44A GLN* 3.4 29.2 - - + +
46A VAL* 4.1 17.7 - - + -
63A VAL* 3.9 16.6 - - + -
65A THR* 4.7 0.4 - - + -
71A CYS* 3.5 32.8 - - + -
72A ALA 3.6 7.4 - - - +
73A LEU* 4.0 12.0 - - + +
106A TYR* 3.9 1.4 - - - -
107A ILE* 2.9 40.8 + - + -
108A ASP* 2.7 27.9 + - + +
123A LEU 4.2 0.6 - - - -
124A ILE* 1.3 71.8 - - - +
126A MET* 1.3 62.2 + - - +
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Residues in contact with MET 126 (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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60A VAL* 4.6 2.0 - - + -
71A CYS* 3.3 10.7 - - - +
72A ALA* 2.7 38.5 + - + +
73A LEU 4.4 0.4 - - - -
74A LYS* 3.7 38.8 - - + +
94A MET* 3.8 27.8 - - + +
104A VAL* 4.6 3.1 - - + -
105A GLY 3.3 11.4 - - - +
106A TYR* 5.1 0.2 - - - -
107A ILE* 3.5 7.3 - - - +
124A ILE* 3.7 18.2 - - + +
125A LEU* 1.3 81.3 - - - +
127A ASP* 1.3 67.6 + - - +
401A LKB 3.2 45.1 - - + +
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Residues in contact with ASP 127 (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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70A LYS 5.6 0.2 - - - -
71A CYS* 5.1 0.2 - - - +
72A ALA* 3.5 1.4 - - - +
104A VAL* 4.0 4.9 - - + +
105A GLY* 2.9 31.2 + - - +
107A ILE* 3.9 13.2 - - - +
126A MET* 1.3 74.3 - - - +
128A PHE* 1.3 56.2 + - - +
185A HIS* 2.8 30.3 + - + +
401A LKB 2.7 32.2 + - - -
67B ASN* 2.6 39.1 + - - +
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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