Contacts of the strand formed by residues 119 - 129 (chain B) in PDB entry 3MIZ
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 GLY 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B PHE* 3.3 10.3 - - - -
63B GLY 2.8 25.1 + - - -
117B ILE* 3.2 4.3 - - - +
118B ASP* 1.3 82.1 - - - +
120B VAL* 1.3 64.4 + - - -
139B ILE* 4.0 1.8 - - - -
140B PRO 3.4 10.8 - - - -
310B LEU* 3.8 7.9 - - - -
314B ILE* 3.6 13.5 - - - -
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 3.2 9.6 - - - +
65B ILE* 3.7 26.0 - - + -
109B TRP* 3.8 24.2 - - + -
112B PHE* 4.5 11.9 - - + -
117B ILE* 4.4 8.1 - - + -
119B GLY* 1.3 78.8 - - - +
121B LEU* 1.3 74.0 + - - +
122B TYR* 4.1 2.2 - - - +
139B ILE* 4.1 20.4 - - + -
140B PRO 2.8 9.3 + - - -
141B THR* 3.3 15.5 - - + +
142B VAL 3.0 25.3 + - - -
310B LEU* 3.7 4.6 - - - +
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Residues in contact with LEU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B PHE* 4.8 8.3 - - + -
63B GLY 2.8 13.4 + - - +
64B ILE* 3.4 15.0 - - + +
65B ILE 3.0 23.4 + - - -
82B ILE* 3.4 49.8 - - + -
120B VAL* 1.3 74.2 - - - +
122B TYR* 1.3 60.5 + - - +
123B VAL* 3.5 3.0 + - + -
142B VAL* 3.5 8.7 - - + +
144B ILE* 3.9 21.3 - - + -
306B GLY 3.9 17.5 - - - +
307B ALA* 4.3 8.3 - - + -
310B LEU* 3.5 29.2 - - + -
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Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ILE* 3.6 25.8 - - + -
67B ASP* 6.1 0.3 - - - +
98B THR* 5.7 1.3 + - + +
105B GLU* 3.5 34.3 + - - -
109B TRP* 3.9 20.0 - + - -
120B VAL* 3.8 3.6 + - + -
121B LEU* 1.3 69.4 - - - +
123B VAL* 1.3 61.5 + - - +
124B THR* 4.2 18.8 - - + -
128B ARG* 5.1 5.2 + - - -
130B VAL* 4.4 21.1 - - + +
132B PRO* 3.8 24.3 - - + +
141B THR* 4.1 11.7 - - + -
142B VAL 3.0 7.7 + - - -
143B MSE 3.4 20.2 - - + -
144B ILE 2.8 26.3 + - - +
146B CYS* 3.7 15.4 - - - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ILE* 4.3 10.3 - - + -
65B ILE 2.9 10.4 + - - +
66B THR* 3.1 37.4 - - + -
67B ASP* 3.6 2.1 + - - -
78B ILE* 3.8 35.0 - - + -
79B VAL* 6.1 1.8 - - + -
82B ILE* 4.4 4.5 - - + -
121B LEU 4.0 10.1 - - - +
122B TYR* 1.3 78.9 - - - +
124B THR* 1.3 77.1 + - - +
125B MSE 4.1 12.6 - - + -
144B ILE* 3.6 29.4 - - + +
145B ASN* 4.9 0.4 - - + -
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Residues in contact with THR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B ASP* 3.2 20.2 - - - +
75B SER* 3.6 1.2 + - - -
122B TYR* 4.2 13.2 - - + -
123B VAL* 1.3 86.7 - - - +
125B MSE 1.3 65.9 + - - +
126B TYR 3.0 15.4 + - - -
128B ARG* 3.7 20.9 - - + +
130B VAL* 4.5 1.6 - - + -
144B ILE 3.6 3.0 + - - -
145B ASN* 2.9 43.0 + - - -
146B CYS* 3.3 24.1 - - + +
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Residues in contact with MSE 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B THR* 3.9 34.3 - - + +
67B ASP* 2.8 31.2 + - - +
68B TYR* 3.6 11.0 - - + +
71B THR* 3.7 35.2 - - + +
72B THR* 5.3 3.8 - - - -
73B PRO 4.2 14.8 - - - +
74B TYR* 4.0 9.3 - - + +
75B SER* 3.0 44.8 + - - +
76B VAL* 5.5 1.8 - - - -
79B VAL* 5.7 5.6 - - + -
123B VAL* 4.1 7.6 - - + -
124B THR* 1.3 76.8 - - - +
126B TYR* 1.3 61.2 + - + +
145B ASN* 3.4 5.0 + - - -
299B TYR* 3.8 5.9 + - - -
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Residues in contact with TYR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 5.2 0.6 + - - -
68B TYR* 3.6 34.0 + + - -
71B THR* 3.6 25.6 - - + -
74B TYR* 4.3 11.4 - + + -
124B THR* 3.0 16.5 + - - -
125B MSE 1.3 77.6 - - + +
127B ARG* 1.3 76.7 + - - +
128B ARG* 3.2 28.6 + - + +
145B ASN* 3.6 6.7 - - - +
188B ILE* 5.8 4.0 - - + +
189B LEU* 3.4 35.7 - - + -
190B LEU 6.1 0.2 - - - -
223B VAL* 3.7 31.3 - - + +
299B TYR* 4.9 2.9 - - - +
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Residues in contact with ARG 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B TYR* 1.3 79.8 - - - +
128B ARG* 1.3 66.2 + - - +
145B ASN* 3.3 22.2 + - - +
147B ARG* 3.0 30.9 - - - +
158B GLU* 3.0 30.0 + - - +
159B PRO* 2.8 28.6 + - + +
160B ASP* 4.2 2.6 + - - +
161B ASP* 2.7 44.7 + - - +
162B TYR 4.8 0.6 - - - +
190B LEU* 3.6 30.8 + - + +
191B GLY* 4.1 15.5 - - - +
194B LEU* 3.7 15.5 - - - +
299B TYR* 5.5 0.4 + - - -
325B VAL* 5.6 1.0 - - - +
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Residues in contact with ARG 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ASP* 2.8 45.0 + - - +
68B TYR* 4.5 13.1 + - - -
100B GLY* 6.2 0.8 - - - -
122B TYR* 5.1 5.1 + - - -
124B THR* 3.7 20.4 - - + +
126B TYR* 3.2 38.5 + - + +
127B ARG* 1.3 78.9 - - - +
129B ILE* 1.3 66.5 + - - +
130B VAL* 3.9 33.9 - - + +
145B ASN 3.6 4.2 + - - -
146B CYS* 3.2 4.1 - - - -
147B ARG* 3.0 24.6 + - - +
158B GLU* 4.4 2.1 - - - +
190B LEU* 4.7 4.5 - - - -
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Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A TYR* 5.1 0.7 - - + -
166A ARG* 3.0 46.9 - - - +
205A GLU* 6.1 1.3 - - - +
128B ARG* 1.3 75.4 + - - +
130B VAL* 1.3 66.1 + - - +
147B ARG* 3.3 29.8 - - + +
149B GLN* 3.1 46.2 + - - +
190B LEU* 3.9 24.0 - - + +
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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