Contacts of the strand formed by residues 120 - 126 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D LYS* 4.1 6.7 - - - -
70D SER 4.9 3.1 - - - -
71D THR* 6.1 1.3 - - - -
118D ASP 3.3 2.6 + - - -
119D GLU* 1.3 78.4 + - - +
121D VAL* 1.3 66.6 + - - -
122D TYR* 3.9 4.5 + - - -
138D LEU 3.4 1.4 - - - +
139D ASN* 4.5 3.6 - - - -
140D LEU* 2.6 48.0 + - - +
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Residues in contact with VAL 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D LYS* 3.5 6.1 - - - +
70D SER* 3.3 42.3 + - - +
72D ASN* 5.7 2.2 - - - +
120D GLY* 1.3 77.4 - - - -
122D TYR* 1.3 63.7 + - - +
123D ILE* 5.7 0.9 - - + -
137D GLN* 2.9 42.2 - - + +
138D LEU 3.3 11.0 - - - +
139D ASN* 3.8 13.5 - - - +
1J NAG 3.4 31.2 - - - +
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Residues in contact with TYR 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D LEU* 4.2 12.8 - - + -
67D TRP* 3.5 19.5 - + + -
68D GLN 3.1 15.5 - - - -
69D LYS* 3.5 24.6 - - + +
78D VAL* 4.0 14.4 - - + -
93D TYR* 3.3 29.7 + + - -
111D LEU* 4.1 6.9 - - + +
118D ASP* 3.2 36.9 + - + +
120D GLY 4.0 3.4 - - - -
121D VAL* 1.3 74.7 - - - +
123D ILE* 1.3 61.4 + - - +
124D CYS 4.1 0.2 + - - -
136D SER 3.6 0.3 - - - +
137D GLN* 3.0 26.7 - - - +
138D LEU* 3.0 30.8 + - + +
140D LEU* 3.8 30.5 - - + -
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66D THR 2.5 26.8 - - - +
67D TRP* 3.3 4.3 - - - -
68D GLN* 2.6 48.0 + - + +
70D SER* 4.4 16.4 - - - +
75D LYS* 4.2 27.4 - - - +
121D VAL* 5.7 0.9 - - + +
122D TYR* 1.3 74.4 - - - +
124D CYS* 1.3 54.5 + - - +
125D GLU* 4.4 6.3 - - + +
135D GLU* 4.2 28.3 - - + +
136D SER 3.4 3.1 - - - +
137D GLN* 3.9 31.2 - - + +
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Residues in contact with CYS 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D VAL* 3.5 8.0 - - - +
35D VAL* 4.0 10.1 - - + -
51D CYS* 2.0 51.4 - - - -
65D VAL* 4.1 14.1 - - - -
66D THR 3.4 2.5 - - - -
67D TRP* 3.5 37.8 - - + -
123D ILE* 1.3 70.0 - - - +
125D GLU* 1.3 58.7 + - - +
126D PHE 4.1 0.2 - - - -
135D GLU* 3.1 20.6 - - - -
136D SER 3.0 13.4 + - - +
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Residues in contact with GLU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A LEU* 3.1 8.3 - - - +
222A ARG* 2.8 24.4 + - - -
65D VAL* 3.5 3.6 - - - -
66D THR* 2.5 77.3 + - - +
68D GLN* 4.7 2.9 - - - +
123D ILE* 4.4 6.3 - - + -
124D CYS* 1.3 72.9 - - - +
126D PHE* 1.3 67.6 + - - +
133D ASN* 2.7 34.0 + - + -
134D ARG 3.1 14.1 - - - +
135D GLU* 3.8 20.8 - - + +
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Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D VAL* 4.4 11.0 - - + -
51D CYS* 4.3 8.7 - - - -
52D SER* 3.4 13.7 - - - -
53D PHE* 3.2 59.5 - + + -
62D ILE* 4.5 13.7 - - + -
64D GLN 3.2 15.3 - - - -
65D VAL* 3.2 26.0 - - + -
103D SER 4.8 3.1 - - - -
104D PHE 4.3 11.4 - - - -
105D THR* 4.5 0.4 - - - -
106D ASP 3.7 25.1 - - - -
107D GLY 4.3 4.9 - - - -
124D CYS 4.1 1.2 + - - -
125D GLU* 1.3 72.6 - - - +
127D ALA* 1.3 59.3 + - - +
128D THR* 3.6 2.4 + - - +
133D ASN* 3.3 17.2 - - - +
134D ARG 3.0 18.8 + - - +
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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