Contacts of the strand formed by residues 118 - 127 (chain A) in PDB entry 3BX7
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 TYR 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A TRP* 3.4 6.9 - - - -
112A SER* 2.6 44.1 + - - -
113A THR* 2.7 33.1 + - - -
114A ASP* 2.9 41.8 + - + +
117A GLN* 1.3 88.5 - - - +
119A ALA* 1.3 64.0 + - - +
120A VAL* 4.2 12.1 - - + -
137A ILE* 4.7 5.6 - - + -
138A TYR 3.2 12.1 - - - +
144A LEU* 4.2 16.6 - - + -
148A LEU* 4.0 26.7 - - + -
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Residues in contact with ALA 119 (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 PHE* 3.6 27.4 - - + -
31A TRP* 3.8 10.8 - - + -
110A VAL* 5.4 0.2 - - + -
112A SER 3.2 8.1 - - - -
113A THR* 3.4 12.6 - - - +
118A TYR* 1.3 79.5 - - - +
120A VAL* 1.3 64.4 + - - +
121A VAL* 4.1 2.0 - - + -
136A THR 3.7 0.3 - - - +
137A ILE* 3.2 4.0 - - - +
138A TYR* 2.7 45.5 + - + +
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Residues in contact with VAL 120 (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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110A VAL* 3.7 1.4 - - - +
111A VAL* 2.7 50.6 + - + -
112A SER* 2.7 19.9 + - - +
118A TYR* 4.2 15.0 - - + -
119A ALA* 1.3 76.7 - - - +
121A VAL* 1.3 60.5 + - - +
135A ILE* 3.9 24.0 - - + -
136A THR 3.3 4.5 - - - +
137A ILE* 4.1 21.5 - - + -
152A PHE* 4.6 6.7 - - + -
155A PHE* 4.1 13.7 - - + -
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Residues in contact with VAL 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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27A PHE* 4.3 17.3 - - + -
56A TYR* 4.9 4.5 - - + +
108A VAL* 3.7 21.3 - - + -
109A ARG 3.6 10.3 - - - +
110A VAL* 4.5 9.9 - - + -
111A VAL* 4.4 2.5 - - - -
119A ALA* 4.6 0.4 - - + -
120A VAL* 1.3 82.3 - - - +
122A PHE* 1.3 64.4 + - - +
123A PHE* 3.6 24.3 - - + -
135A ILE* 3.3 5.6 - - - +
136A THR* 2.9 42.2 + - + -
138A TYR* 3.6 26.9 - - + -
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Residues in contact with PHE 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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11A PRO* 4.2 12.3 - - + -
13A LEU* 4.0 22.7 - - + -
16A VAL* 3.7 43.7 - - + -
107A LEU* 4.5 6.5 - - + -
108A VAL* 3.4 5.4 - - - -
109A ARG* 2.8 47.0 + - + +
111A VAL* 3.9 2.4 - - + +
121A VAL* 1.3 75.9 - - - +
123A PHE* 1.3 64.8 + - - +
124A LYS* 3.5 34.1 - - + -
133A PHE* 4.0 26.5 - + + -
134A ALA 3.5 5.4 - - - -
135A ILE* 3.1 28.9 - - + -
159A LEU* 4.4 0.9 - - + -
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Residues in contact with PHE 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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56A TYR* 4.4 0.7 - - - -
83A PHE* 4.0 24.5 - + - -
106A TYR* 3.4 22.0 - - + +
107A LEU 3.4 4.3 - - - -
108A VAL* 4.1 6.7 - - + -
121A VAL* 3.6 25.1 - - + -
122A PHE* 1.3 79.1 - - - +
124A LYS* 1.3 61.1 + - - +
125A LEU 4.3 0.2 - - - -
132A PHE 4.5 0.2 - - - -
133A PHE* 3.0 8.3 - - - +
134A ALA 2.8 43.1 + - - +
135A ILE 4.8 0.2 - - - -
136A THR* 3.6 27.4 - - + -
138A TYR* 3.8 19.5 - - - -
102C PRO* 4.1 11.9 - - + +
103C PRO* 3.8 36.6 - - + -
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Residues in contact with LYS 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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10A ALA* 3.9 16.9 - - + +
11A PRO 4.9 4.2 + - - +
13A LEU* 4.3 31.5 - - + +
105A SER* 3.7 1.3 - - - +
106A TYR* 3.3 9.2 - - - -
107A LEU* 2.9 44.4 + - + +
122A PHE* 3.5 21.8 - - + -
123A PHE* 1.3 75.3 - - - +
125A LEU* 1.3 66.4 + - - +
126A ALA* 4.4 13.5 - - + +
131A GLU* 3.5 28.2 + - + -
132A PHE 3.5 7.0 - - - +
133A PHE* 4.4 5.2 - - + -
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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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40A ARG* 4.8 4.9 - - - +
94A LEU* 5.7 1.6 - - + -
97A ILE* 5.6 0.7 - - + -
104A THR* 4.2 18.6 - - + -
105A SER 3.6 12.3 - - - +
106A TYR* 4.1 22.2 - - + -
123A PHE 4.3 0.2 - - - -
124A LYS* 1.3 72.8 - - - +
126A ALA* 1.3 59.9 + - - +
127A GLU* 4.2 15.5 - - + +
131A GLU* 3.4 2.3 - - - +
132A PHE* 2.7 60.2 + - + +
31C ALA* 4.3 10.8 - - + -
32C THR* 3.5 24.7 - - - +
101C PRO* 4.2 18.4 - - + -
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Residues in contact with ALA 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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103A LYS 3.6 2.6 - - - +
104A THR* 3.2 8.5 - - - +
105A SER* 2.8 53.3 + - - +
124A LYS* 3.9 16.7 + - + -
125A LEU* 1.3 72.7 - - - +
127A GLU* 1.3 63.6 + - - +
130A ALA 3.8 3.4 - - - -
131A GLU* 4.4 16.6 - - + +
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Residues in contact with GLU 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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103A LYS 3.6 9.8 - - - +
104A THR* 4.4 11.9 - - - +
125A LEU* 4.2 12.6 - - + +
126A ALA* 1.3 81.6 - - - +
128A ASP* 1.3 71.1 + - - +
129A ASN 3.2 3.7 + - - +
130A ALA* 2.8 24.9 + - + +
131A GLU* 5.3 1.6 - - - +
132A PHE* 3.7 17.5 - - + -
29C GLY* 3.4 8.3 - - - -
30C LYS* 2.8 34.4 + - + +
31C ALA* 2.6 38.8 + - - +
32C THR 4.3 0.2 + - - -
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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