Contacts of the strand formed by residues 120 - 128 (chain B) in PDB entry 3A2C
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 ILE 120 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105B VAL* 4.3 7.2 - - + +
108B HIS* 3.3 54.3 - - + +
109B TRP* 3.6 45.8 - - + +
112B SER* 3.5 6.0 + - - +
119B ARG* 1.3 86.3 + - - +
121B VAL* 1.3 64.0 + - - +
122B ASP 3.7 11.4 - - - +
123B VAL* 3.6 29.8 - - + -
136B ILE* 4.0 15.5 - - + -
137B VAL 3.6 5.4 - - - +
138B MET* 4.4 0.7 - - + -
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Residues in contact with VAL 121 (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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63B TYR* 3.9 11.9 - - - +
90B PHE* 3.5 35.7 - - + -
109B TRP* 4.8 7.8 - - - -
119B ARG* 4.2 20.4 - - - +
120B ILE* 1.3 77.0 - - - +
122B ASP* 1.3 83.1 + - - +
137B VAL* 2.7 21.1 + - + +
139B GLU* 4.0 11.9 - - - +
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Residues in contact with ASP 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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53B GLN* 5.8 0.5 + - - -
55B LYS* 3.0 43.7 + - + +
63B TYR* 3.4 11.4 + - - -
109B TRP* 6.0 0.7 - - - -
120B ILE* 3.7 2.7 - - - +
121B VAL* 1.3 100.6 - - + +
123B VAL* 1.3 66.9 + - - +
124B TYR* 3.9 17.1 + - + -
135B LEU 4.1 0.2 - - - +
137B VAL* 3.1 29.4 + - + +
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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
----------------------------------------------------------
52B LEU* 3.7 20.9 - - + +
53B GLN 4.3 3.7 + - - +
54B ILE* 3.5 20.3 - - + -
55B LYS* 2.9 27.9 + - - +
105B VAL* 3.5 37.2 - - + -
120B ILE* 3.6 18.8 - - + -
122B ASP* 1.3 80.1 - - - +
124B TYR* 1.3 72.4 + - - +
134B LEU* 4.3 8.7 - - + -
135B LEU 3.5 7.6 - - - +
136B ILE* 4.7 7.4 - - + -
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Residues in contact with TYR 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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54B ILE* 3.9 2.2 - - - -
55B LYS* 3.4 27.0 - - + +
57B ASN* 3.2 38.1 - - - -
59B ILE* 3.3 49.1 - - + -
62B ASP* 3.1 30.1 + - - +
63B TYR* 3.6 13.2 - + - -
122B ASP* 3.9 16.1 + - + -
123B VAL* 1.3 78.1 - - - +
125B GLU* 1.3 57.9 + - - +
126B ASN* 4.1 2.5 - - - +
134B LEU* 3.2 10.9 - - - +
135B LEU* 2.8 52.7 + - + -
137B VAL* 4.2 6.5 - - + -
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Residues in contact with GLU 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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54B ILE* 3.5 18.0 - - + +
55B LYS 2.9 8.1 + - - -
56B LYS* 2.9 42.3 + - + +
97B ASP* 4.4 3.4 - - - +
102B ARG* 2.8 33.8 + - - +
124B TYR* 1.3 72.2 - - - +
126B ASN* 1.3 73.3 + - - +
132B LYS* 4.5 28.4 + - + +
133B CYS 3.7 7.4 - - - +
134B LEU* 4.2 4.3 - - + -
51E GLY* 3.3 25.8 + - - -
52E LEU 4.5 1.7 + - - -
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Residues in contact with ASN 126 (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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56B LYS 3.6 4.8 + - - -
57B ASN 2.8 22.3 + - - -
58B ALA* 3.5 3.2 - - - -
59B ILE 3.0 25.7 + - - -
124B TYR* 4.1 2.0 - - - +
125B GLU* 1.3 100.3 + - - +
127B LEU* 1.3 66.2 + - - +
128B TYR 3.7 0.3 + - - -
131B ARG 3.8 0.7 - - - +
132B LYS* 3.9 3.5 - - - +
133B CYS* 3.2 33.3 + - - +
135B LEU* 3.7 20.8 - - + +
48E VAL* 3.4 24.3 - - + +
49E LYS 3.4 10.3 - - - +
50E SER* 4.0 0.8 - - - +
51E GLY* 4.2 2.9 - - - +
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Residues in contact with LEU 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 ASN* 1.3 77.4 - - - +
128B TYR* 1.3 58.9 + - - +
129B ALA 4.3 0.2 - - - -
130B GLY* 4.6 3.6 - - - -
131B ARG 3.5 11.4 - - - +
132B LYS* 4.0 17.0 - - + -
48E VAL* 3.1 8.8 - - - +
49E LYS* 2.5 39.7 + - + +
50E SER 3.1 26.7 - - - +
51E GLY* 4.4 4.5 - - - -
106E GLU* 5.4 0.4 - - - +
109E TRP* 3.4 25.4 - - + +
110E ARG* 4.0 32.5 - - + -
113E GLN* 4.2 29.6 + - + +
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Residues in contact with TYR 128 (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 SER* 3.8 9.9 + - - -
70B LEU* 3.3 53.2 - - + +
71B GLY* 3.9 3.3 + - - -
74B ILE* 4.2 32.3 - - + -
94B MET* 5.1 3.1 - - + -
126B ASN 3.7 0.8 + - - -
127B LEU* 1.3 73.4 - - - +
129B ALA* 1.3 82.1 + - + +
130B GLY 2.9 0.2 - - - -
131B ARG* 2.9 24.9 + - - +
133B CYS* 3.5 23.6 - - - -
48E VAL* 4.0 23.1 - - + +
273F PRO* 4.4 14.9 - - + +
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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