Contacts of the strand formed by residues 120 - 128 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69F LYS* 5.3 3.6 - - - -
70F SER 5.4 2.0 - - - -
71F THR* 5.9 3.1 - - - -
118F ASP 3.8 0.8 + - - -
119F GLU* 1.3 75.9 - - - +
121F VAL* 1.3 62.3 + - - -
122F TYR* 5.0 2.0 - - - -
139F ASN* 3.8 8.3 - - - -
140F LEU* 2.5 49.1 + - - +
1L NAG 5.5 2.2 - - - -
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Residues in contact with VAL 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69F LYS* 4.0 3.1 - - - +
70F SER* 3.4 42.7 + - - +
72F ASN* 5.5 5.8 - - + +
120F GLY* 1.3 73.8 - - - -
122F TYR* 1.3 64.1 - - - +
123F ILE* 5.3 0.7 - - - -
137F GLN* 3.1 44.6 - - + +
138F LEU 3.6 8.7 - - - +
139F ASN* 3.8 13.0 - - - +
1L NAG 3.6 32.3 - - - +
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Residues in contact with TYR 122 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F LEU* 4.8 7.2 - - + -
67F TRP* 4.1 16.5 - + + -
68F GLN 3.4 15.0 - - - -
69F LYS* 3.4 43.4 + - + +
78F VAL* 4.2 11.0 - - + -
93F TYR* 2.8 29.4 + + - -
111F LEU* 4.0 13.6 - - + +
118F ASP* 3.5 27.2 + - - +
120F GLY 3.8 1.5 + - - -
121F VAL* 1.3 74.7 - - - +
123F ILE* 1.3 61.3 + - - +
124F CYS 4.1 0.6 + - - -
137F GLN* 3.2 7.7 - - - +
138F LEU* 2.8 50.5 + - + +
140F LEU* 3.8 28.3 - - + -
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Residues in contact with ILE 123 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F THR* 3.2 4.7 - - - +
67F TRP* 4.1 2.9 - - - -
68F GLN* 2.6 55.1 + - + +
69F LYS 5.3 0.2 - - - -
70F SER* 3.7 30.7 - - - +
75F LYS* 4.1 19.7 - - + +
121F VAL 5.3 0.7 - - - +
122F TYR* 1.3 76.5 - - - +
124F CYS* 1.3 65.9 + - - +
125F GLU* 3.8 2.1 + - + +
135F GLU* 2.9 37.9 - - - +
136F SER 3.8 3.1 - - - +
137F GLN* 3.1 35.2 - - + +
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Residues in contact with CYS 124 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F VAL* 4.8 0.9 - - - +
35F VAL* 4.6 9.4 - - + -
51F CYS* 2.0 51.1 - - - -
65F VAL* 4.5 12.6 - - - -
66F THR 3.3 8.3 - - - -
67F TRP* 3.8 29.0 - - + -
107F GLY 4.3 1.8 - - - -
122F TYR 4.1 0.8 + - - -
123F ILE* 1.3 73.3 - - - +
125F GLU* 1.3 63.0 + - - +
126F PHE 4.4 0.2 - - - -
135F GLU* 3.0 25.5 - - - +
136F SER 3.3 9.3 + - - +
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Residues in contact with GLU 125 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220B LEU* 3.6 10.6 - - - +
222B ARG* 2.7 38.6 + - - +
64F GLN 4.8 0.2 - - - -
65F VAL* 3.8 0.9 - - - -
66F THR* 2.9 42.8 + - + +
68F GLN* 5.0 3.8 - - - +
123F ILE* 4.9 2.7 - - + -
124F CYS* 1.3 76.6 - - - +
126F PHE* 1.3 67.7 + - - +
127F ALA* 3.8 2.1 + - - +
133F ASN* 4.9 8.8 + - - +
134F ARG 3.2 18.8 - - - +
135F GLU* 3.9 21.8 - - + +
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Residues in contact with PHE 126 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F VAL* 3.6 22.8 - - + +
51F CYS* 4.3 5.2 - - - -
52F SER* 3.3 12.8 - - - -
53F PHE* 3.2 50.6 - + + -
62F ILE* 4.4 7.6 - - + -
64F GLN 3.8 3.4 - - - -
65F VAL* 3.1 35.4 - - + -
104F PHE 2.9 28.5 - - - -
105F THR 3.9 1.1 - - - -
106F ASP* 3.6 22.2 - - - -
107F GLY 4.0 4.5 - - - -
124F CYS 4.4 0.4 - - - -
125F GLU* 1.3 74.9 - - - +
127F ALA* 1.3 60.4 + - - +
128F THR* 4.5 4.3 - - + +
132F GLY 5.0 0.2 - - - +
133F ASN* 3.6 5.5 - - - +
134F ARG 3.0 28.4 + - - +
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Residues in contact with ALA 127 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B ARG* 4.0 28.0 - - - +
223B PHE* 4.9 4.7 - - + -
62F ILE* 3.2 3.1 - - - +
63F THR* 2.6 35.9 + - + +
64F GLN* 2.8 39.0 + - + +
125F GLU 3.8 1.9 + - - +
126F PHE* 1.3 70.3 - - - +
128F THR* 1.3 63.5 + - - +
133F ASN* 3.4 4.7 - - - +
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Residues in contact with THR 128 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 3.0 22.7 - - - -
231B VAL* 4.3 1.7 - - - +
53F PHE* 4.4 21.5 - - + -
61F LYS 3.3 6.5 - - - -
62F ILE* 3.3 32.5 - - + -
63F THR* 3.5 1.9 - - - +
126F PHE 4.5 2.2 - - - +
127F ALA* 1.3 84.0 - - - +
129F PHE* 1.4 60.0 + - - +
130F PRO* 3.3 14.7 - - - +
131F THR* 2.8 42.3 + - - +
132F GLY 3.9 4.7 + - - -
133F ASN* 3.3 12.0 + - - +
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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