Contacts of the strand formed by residues 119 - 129 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A THR 3.9 1.8 + - - -
62A PHE* 3.6 3.0 - - - -
63A GLY 2.9 23.7 + - - -
117A ILE* 2.9 7.6 - - - +
118A ASP* 1.3 81.0 - - - +
120A VAL* 1.3 63.6 + - - -
139A ILE* 3.8 3.6 - - - -
140A PRO 3.3 12.1 - - - -
310A LEU* 3.8 7.6 - - - -
314A ILE* 3.9 14.5 - - - +
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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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63A GLY 3.1 9.2 - - - +
65A ILE* 3.9 16.2 - - + -
109A TRP* 3.8 33.7 - - + -
112A PHE* 4.1 20.6 - - + -
117A ILE* 4.7 3.1 - - + -
119A GLY* 1.3 77.8 - - - +
121A LEU* 1.3 78.4 + - - +
122A TYR* 3.9 3.6 - - - +
139A ILE* 4.3 13.2 - - + -
140A PRO 2.9 7.3 + - - -
141A THR* 3.3 14.2 - - + +
142A VAL 3.0 24.9 + - - -
310A LEU* 3.7 5.7 - - - +
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Residues in contact with LEU 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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62A PHE* 4.4 9.6 - - + -
63A GLY 2.8 11.9 + - - +
64A ILE* 3.3 12.7 - - + +
65A ILE 3.0 21.5 + - - -
82A ILE* 3.3 43.7 - - + -
120A VAL* 1.3 72.0 - - - +
122A TYR* 1.3 62.8 + - - +
123A VAL* 3.4 7.7 + - + -
142A VAL* 3.4 11.4 - - + +
144A ILE* 3.7 26.2 - - + -
306A GLY 3.7 18.6 - - - +
307A ALA* 4.2 7.9 - - + -
310A LEU* 3.6 27.8 - - + -
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Residues in contact with TYR 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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65A ILE* 3.6 24.0 - - + -
98A THR* 5.6 1.4 - - + +
105A GLU* 3.0 42.0 + - - -
109A TRP* 3.9 19.3 - + - -
120A VAL* 3.8 3.1 - - + -
121A LEU* 1.3 69.3 - - - +
123A VAL* 1.3 60.7 + - - +
124A THR* 4.4 10.5 - - + -
128A ARG* 5.3 4.3 + - - -
130A VAL* 4.3 26.0 - - + +
131A ASP 4.6 1.6 + - - -
132A PRO* 3.7 24.3 - - + +
141A THR* 4.2 8.5 - - + -
142A VAL 3.0 7.9 + - - +
143A MSE 3.4 22.1 - - + -
144A ILE 2.8 27.4 + - - +
146A CYS* 3.7 17.5 - - - -
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Residues in contact with VAL 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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64A ILE* 4.0 20.2 - - + -
65A ILE 2.9 9.8 + - - +
66A THR* 3.1 29.6 + - - +
67A ASP 3.6 1.6 + - - -
78A ILE* 3.7 41.1 - - + -
79A VAL* 5.8 3.4 - - + -
82A ILE* 5.5 1.1 - - + -
121A LEU* 3.7 16.4 - - + +
122A TYR* 1.3 77.6 - - - +
124A THR* 1.3 69.9 + - - +
125A MSE 4.4 10.1 - - + -
144A ILE* 3.4 27.4 - - + +
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Residues in contact with THR 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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67A ASP* 3.5 20.4 - - + +
78A ILE* 4.3 2.1 - - - +
122A TYR* 4.2 13.0 + - + -
123A VAL* 1.3 83.9 - - - +
125A MSE 1.3 66.5 + - - +
126A TYR 2.9 22.3 + - - -
128A ARG* 3.8 18.8 - - + +
130A VAL* 4.6 1.1 - - + -
144A ILE 3.4 3.8 + - - -
145A ASN* 2.9 37.2 + - - +
146A CYS* 3.3 25.9 - - + +
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Residues in contact with MSE 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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66A THR* 3.1 25.1 - - - +
67A ASP* 2.9 15.7 + - - +
68A TYR* 3.3 31.9 - - + +
69A VAL* 3.5 17.5 - - + +
72A THR* 3.0 42.1 - - + +
75A SER* 2.6 48.6 + - - +
76A VAL 5.1 0.4 - - - -
79A VAL* 5.4 7.2 - - + -
123A VAL* 4.4 10.8 - - + -
124A THR* 1.3 78.0 - - - +
126A TYR* 1.3 66.3 + - + +
145A ASN* 3.5 7.2 - - - +
299A TYR* 3.6 4.2 + - - -
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Residues in contact with TYR 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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67A ASP* 5.2 0.4 + - - -
68A TYR* 3.4 38.7 + + - -
72A THR* 5.0 7.6 - - + -
124A THR* 2.9 19.9 + - - -
125A MSE 1.3 84.5 - - + +
127A ARG* 1.3 72.7 + - - +
128A ARG* 3.2 29.2 + - + +
145A ASN* 3.6 6.5 - - - -
188A ILE* 6.0 1.7 - - - +
189A LEU* 3.4 36.3 - - + -
223A VAL* 3.8 33.2 - - + +
299A TYR* 4.8 2.7 - - - -
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Residues in contact with ARG 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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126A TYR* 1.3 79.7 - - - +
128A ARG* 1.3 66.0 + - - +
145A ASN* 3.1 25.4 + - - +
147A ARG* 4.2 10.7 - - - +
158A GLU* 3.0 35.5 + - + +
159A PRO* 3.0 26.6 + - + -
160A ASP* 4.3 2.2 + - - +
161A ASP* 2.9 38.8 + - - +
162A TYR* 4.8 1.0 - - - +
189A LEU* 5.5 0.2 - - - +
190A LEU* 3.8 32.1 + - + +
191A GLY* 4.6 12.9 + - - +
194A LEU* 3.5 25.5 - - - +
299A TYR* 5.4 0.6 + - - -
325A VAL* 4.9 10.3 - - - +
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Residues in contact with ARG 128 (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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67A ASP* 2.8 46.3 + - - +
68A TYR* 4.4 11.5 + - - -
100A GLY* 5.7 1.8 - - - -
122A TYR* 5.3 4.9 + - - -
124A THR* 3.8 16.0 - - + +
126A TYR* 3.2 38.5 + - + +
127A ARG* 1.3 76.6 - - - +
129A ILE* 1.3 67.2 + - - +
130A VAL* 3.7 40.4 - - + +
145A ASN 3.5 4.4 + - - -
146A CYS* 3.1 4.6 - - - -
147A ARG 2.9 23.9 + - - -
158A GLU* 4.3 2.6 - - - +
190A LEU* 4.9 4.5 - - - -
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Residues in contact with ILE 129 (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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128A ARG* 1.3 75.9 + - - +
130A VAL* 1.3 65.9 + - - +
147A ARG* 3.0 38.8 - - - +
148A PRO 3.9 4.0 - - - +
149A GLN* 3.6 41.7 + - - +
190A LEU* 4.0 19.0 - - + +
162B TYR* 5.1 0.7 - - + -
166B ARG* 3.1 43.5 - - - +
205B GLU* 5.7 4.5 - - - +
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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