Contacts of the strand formed by residues 120 - 128 (chain E) in PDB entry 3SKU
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 120 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69E LYS* 4.1 9.2 - - - -
70E SER 5.1 1.6 - - - -
118E ASP 2.9 3.4 + - - -
119E GLU* 1.3 76.6 - - - +
121E VAL* 1.3 59.8 + - - -
122E TYR* 3.4 9.1 - - - -
139E ASN* 4.5 1.8 - - - -
140E LEU* 2.5 45.2 + - - -
1H NAG 6.2 0.2 - - - -
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Residues in contact with VAL 121 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69E LYS* 3.8 1.7 - - - +
70E SER* 3.4 46.2 + - - +
120E GLY* 1.3 73.2 - - - -
122E TYR* 1.3 67.1 + - - +
123E ILE* 5.0 0.7 - - + -
137E GLN* 3.8 34.5 - - + +
138E LEU* 3.1 16.6 - - - +
139E ASN* 2.8 34.1 - - - +
1H NAG 4.6 8.1 - - - +
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Residues in contact with TYR 122 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49E LEU* 4.2 13.9 - - + -
67E TRP* 3.9 18.4 - + + -
68E GLN 3.9 8.7 - - - -
69E LYS* 3.4 34.4 + - + +
78E VAL* 4.6 21.1 - - + -
93E TYR* 4.0 15.0 + + - -
111E LEU* 4.7 14.1 - - + +
118E ASP* 3.3 40.6 + - + +
120E GLY 3.4 9.6 - - - -
121E VAL* 1.3 80.4 - - - +
123E ILE* 1.3 61.3 + - - +
124E CYS 4.1 0.3 + - - -
137E GLN* 3.0 5.8 - - - -
138E LEU* 2.7 49.7 + - + +
140E LEU* 4.3 7.0 - - + -
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Residues in contact with ILE 123 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66E THR 3.3 1.0 - - - +
67E TRP* 3.1 29.1 - - - -
68E GLN* 3.1 31.2 + - + +
70E SER* 4.3 21.5 - - - +
75E LYS* 4.2 28.0 - - + -
121E VAL* 5.0 1.6 - - + -
122E TYR* 1.3 75.8 - - - +
124E CYS* 1.3 72.0 + - - +
125E GLU* 4.4 6.1 - - + +
135E GLU* 4.0 25.8 - - + +
136E SER 3.8 2.9 - - - +
137E GLN* 4.0 28.0 - - + +
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Residues in contact with CYS 124 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 4.2 2.2 - - + +
35E VAL* 4.4 6.3 - - + -
51E CYS* 2.0 53.8 - - + -
65E VAL* 4.1 17.5 - - - -
66E THR 3.5 2.5 - - - -
67E TRP* 3.9 24.1 - - + -
122E TYR 4.1 1.0 + - - -
123E ILE* 1.3 73.7 - - - +
125E GLU* 1.3 62.1 + - - +
135E GLU* 3.1 4.0 - - - +
136E SER 2.9 39.3 + - - +
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Residues in contact with GLU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C LEU* 4.2 1.7 - - - +
222C ARG* 2.6 28.5 + - - -
33E VAL* 5.2 0.7 - - - -
65E VAL* 3.5 4.4 - - - +
66E THR* 3.0 45.1 + - - +
68E GLN* 3.7 17.8 - - - +
123E ILE* 4.6 5.8 - - + +
124E CYS* 1.3 76.1 - - - +
126E PHE* 1.3 68.6 + - - +
127E ALA* 5.0 0.8 - - + +
133E ASN* 2.5 34.0 + - - +
134E ARG 3.1 15.0 - - - +
135E GLU* 3.9 14.3 - - + +
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Residues in contact with PHE 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E VAL* 3.7 17.6 - - + +
51E CYS* 3.9 13.9 - - - -
52E SER* 3.4 9.9 - - - -
53E PHE* 3.3 49.0 - + + -
62E ILE* 3.5 20.6 - - + -
64E GLN 3.7 2.5 - - - -
65E VAL* 2.9 30.7 - - + -
103E SER 4.5 0.4 - - - -
104E PHE 3.4 22.2 - - - -
105E THR* 3.7 0.4 - - - -
106E ASP* 3.2 32.1 - - - -
107E GLY 3.7 1.3 - - - -
125E GLU* 1.3 77.9 - - - +
127E ALA* 1.3 58.7 + - - +
128E THR* 4.1 4.8 + - + -
133E ASN* 3.4 12.5 - - - +
134E ARG* 3.3 16.3 + - - +
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Residues in contact with ALA 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ARG* 3.9 26.2 - - - +
223C PHE* 4.7 6.7 - - + -
62E ILE* 3.5 2.0 - - - -
63E THR* 2.7 38.7 + - + -
64E GLN* 2.9 36.8 + - + +
66E THR* 5.9 0.9 - - - +
125E GLU* 5.0 1.1 - - + +
126E PHE* 1.3 73.9 - - - +
128E THR* 1.3 58.3 + - - +
133E ASN* 3.7 4.7 - - - -
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Residues in contact with THR 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223C PHE* 3.2 22.7 - - - -
231C VAL* 4.3 1.7 - - - +
53E PHE* 4.8 18.7 - - + -
60E VAL* 3.5 24.7 - - + -
61E LYS 3.7 1.3 - - - -
62E ILE* 3.5 35.0 - - + -
126E PHE 4.5 4.9 + - - -
127E ALA* 1.3 72.8 - - - +
129E PHE* 1.4 59.3 - - - +
130E PRO* 3.7 1.1 - - - +
131E THR* 2.4 47.5 + - - -
132E GLY* 4.8 0.9 - - - -
133E ASN* 4.1 7.4 + - - +
134E ARG* 5.6 0.3 + - - +
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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