Contacts of the strand formed by residues 109 - 116 (chain A) 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 PRO 109 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LEU* 3.3 31.2 - - + -
99A TRP 3.6 5.8 - - - +
100A PHE* 4.0 5.4 - - + -
108A ILE* 1.3 93.0 - - + +
110A ILE* 1.3 62.2 + - - +
112A VAL* 4.8 3.1 - - + -
136A ASN* 3.9 11.3 + - - +
201A ALA 4.7 0.9 - - - +
203A LEU* 3.5 13.7 - - + -
208A TYR* 3.2 21.3 - - - +
217A ILE* 3.3 31.5 - - + +
219A MET* 3.8 14.5 - - + +
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Residues in contact with ILE 110 (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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99A TRP* 2.7 20.1 + - + +
100A PHE* 3.9 4.3 - - - +
101A ARG* 3.5 32.5 - - + +
108A ILE* 4.0 4.0 - - + +
109A PRO* 1.3 72.4 - - - +
111A THR* 1.3 58.3 + - - +
135A TRP* 3.2 12.1 - - + -
136A ASN 3.0 32.7 + - - +
138A TYR* 3.2 69.5 - - + -
151A PHE* 4.2 9.4 - - + -
164A TYR* 4.0 11.7 - - + -
219A MET* 3.2 7.7 - - - +
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Residues in contact with THR 111 (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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97A ILE 5.3 1.3 - - - +
98A ALA* 3.5 3.5 - - - -
99A TRP* 2.9 61.0 + - + +
110A ILE* 1.3 80.1 - - - +
112A VAL* 1.3 68.6 + - - +
113A MET* 4.9 18.4 - - + +
134A ARG 2.9 6.3 + - - -
135A TRP* 2.9 49.9 + - + -
144A VAL* 5.1 1.8 - - + -
151A PHE* 4.4 2.0 - - + -
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Residues in contact with VAL 112 (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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44A LEU* 3.7 28.5 - - + -
45A PRO* 5.1 2.9 - - + -
96A THR* 4.6 6.7 - - + -
97A ILE 3.6 5.4 - - - +
98A ALA* 5.2 4.5 - - + -
109A PRO* 4.8 2.9 - - + -
111A THR* 1.3 80.5 + - - +
113A MET* 1.3 67.8 + - - +
114A GLU* 4.0 28.0 - - + +
131A THR* 4.1 1.6 + - - -
133A PRO* 3.6 1.4 - - - +
134A ARG* 2.7 50.3 + - + +
214A VAL* 4.1 3.6 - - + -
219A MET* 3.6 30.5 - - + -
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Residues in contact with MET 113 (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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96A THR* 3.3 4.7 - - - +
97A ILE* 2.8 50.2 + - + +
111A THR* 4.9 11.7 - - + +
112A VAL* 1.3 83.1 - - - +
114A GLU* 1.3 62.0 + - - +
115A TYR* 4.1 29.8 - - + +
131A THR* 3.3 6.1 - - - +
133A PRO* 3.7 33.2 - - + -
135A TRP* 5.6 1.6 - - - -
144A VAL* 3.5 35.2 - - + -
148A ASN* 4.0 15.3 - - - +
225A PRO* 4.5 13.5 - - - -
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Residues in contact with GLU 114 (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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40A ILE* 3.2 13.7 + - + +
41A GLN* 2.8 50.9 + - + +
43A GLY 4.1 12.1 - - - +
44A LEU* 5.1 1.7 - - - +
45A PRO* 4.9 3.5 - - - +
95A LEU 3.6 6.5 - - - +
96A THR* 4.1 12.9 - - + +
112A VAL* 4.0 21.1 - - + +
113A MET* 1.3 79.2 - - - +
115A TYR* 1.3 65.8 + - - +
130A ARG* 3.6 1.7 - - - -
131A THR* 2.4 56.9 + - + +
134A ARG* 6.4 0.2 - - + -
214A VAL* 6.1 0.2 - - - +
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Residues in contact with TYR 115 (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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36A ARG* 5.4 3.6 - - - -
40A ILE* 4.3 4.2 - - - +
41A GLN* 5.4 1.4 + - - +
94A ASN* 3.6 5.7 - - - +
95A LEU* 2.8 67.1 + - + +
97A ILE* 3.9 13.4 - - + +
113A MET* 4.1 32.9 - - + +
114A GLU* 1.3 80.0 - - - +
116A THR* 1.3 63.7 + - - +
118A CYS* 3.7 19.7 - - - -
125A GLY* 4.0 27.8 - - - -
127A CYS* 4.2 2.7 - - + -
129A ILE 3.7 4.3 - - - -
130A ARG* 4.4 24.9 - - + -
131A THR 5.9 0.2 - - - -
148A ASN* 4.3 22.9 + - + +
225A PRO* 5.6 1.9 - - - +
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Residues in contact with THR 116 (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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40A ILE* 4.0 22.6 - - + +
93A TYR 4.0 3.6 - - - -
94A ASN* 2.7 22.4 + - - -
115A TYR* 1.3 77.3 - - - +
117A GLU* 1.3 75.0 + - + +
118A CYS* 3.3 2.8 + - - -
127A CYS* 3.8 2.1 - - - +
128A PRO* 3.7 9.4 - - - +
129A ILE* 3.2 49.7 + - + +
1G NAG 4.3 7.8 + - - -
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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