Contacts of the strand formed by residues 95 - 101 (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 LEU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLN* 5.8 0.3 - - - +
93A TYR* 3.7 21.0 - - + -
94A ASN* 1.3 71.8 - - - +
96A THR* 1.3 78.5 + - - +
97A ILE* 3.9 13.2 - - + -
114A GLU* 3.6 0.5 - - - +
115A TYR* 2.8 68.3 + - + +
124A LEU* 3.9 23.6 - - + -
125A GLY* 4.5 6.5 - - - +
168A VAL* 3.7 23.8 - - + -
169A LYS 3.5 2.7 - - - +
170A ILE* 3.4 26.2 - - + +
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Residues in contact with THR 96 (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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41A GLN* 4.5 10.0 - - - +
45A PRO* 4.4 22.0 - - + -
94A ASN 4.7 1.6 + - - -
95A LEU* 1.3 80.9 + - - +
97A ILE* 1.3 70.1 + - - +
112A VAL* 4.6 4.9 - - + -
113A MET 3.3 12.8 - - - +
114A GLU* 4.1 27.1 + - + +
167A LEU* 3.5 4.7 - - - +
168A VAL* 3.5 0.9 - - - -
169A LYS* 2.8 50.4 + - - +
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Residues in contact with ILE 97 (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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95A LEU* 3.9 26.0 - - + -
96A THR* 1.3 76.0 - - - +
98A ALA* 1.3 65.8 + - - +
99A TRP* 4.6 19.5 - - + +
111A THR* 3.9 1.6 - - - +
112A VAL* 3.6 3.1 - - - -
113A MET* 2.8 49.9 + - + +
115A TYR* 3.9 15.3 - - + +
124A LEU* 5.8 0.2 - - + -
148A ASN* 3.8 28.3 - - + +
149A LEU* 4.3 18.4 - - + -
166A ARG* 4.8 5.8 - - + -
167A LEU 3.1 10.5 - - - +
168A VAL* 4.2 11.9 - - + -
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Residues in contact with ALA 98 (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* 6.1 0.2 - - + -
45A PRO* 4.0 18.2 - - + -
96A THR* 4.9 2.0 - - + -
97A ILE* 1.3 77.6 - - - +
99A TRP* 1.3 63.8 + - - +
100A PHE* 3.3 25.7 - - + -
111A THR 3.5 6.1 - - - +
112A VAL* 5.2 5.6 - - + -
165A LEU 3.4 1.6 - - - +
166A ARG* 3.3 4.7 - - - -
167A LEU* 2.7 48.2 + - + +
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Residues in contact with TRP 99 (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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71A LEU* 3.7 28.9 - - + -
97A ILE* 4.6 11.7 - - + +
98A ALA* 1.3 75.2 - - - +
100A PHE* 1.3 63.3 + - - +
109A PRO* 3.6 2.3 - - - +
110A ILE* 2.7 32.3 + - + -
111A THR* 2.9 42.0 + - + +
144A VAL* 5.2 4.8 - - + +
149A LEU 3.9 13.3 + - - -
150A GLY 4.5 2.8 + - - -
151A PHE* 3.5 47.4 - + + +
164A TYR* 4.2 7.2 - + + -
165A LEU 3.3 22.4 - - - -
166A ARG* 3.6 35.8 - - + +
179A PHE* 3.4 37.0 - + - -
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Residues in contact with PHE 100 (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* 4.2 8.3 - - + -
45A PRO* 4.1 13.5 - - + -
47A PRO* 3.7 27.1 - - + -
98A ALA* 3.3 38.8 - - + -
99A TRP* 1.3 76.8 - - - +
101A ARG* 1.3 61.9 + - - +
102A MET* 3.4 11.8 + - - -
107A ALA* 4.0 9.0 - - + -
108A ILE 2.9 22.7 - - - +
109A PRO* 4.0 10.3 - - + -
110A ILE* 3.9 3.3 - - - +
112A VAL* 6.4 0.4 - - + -
164A TYR* 3.6 3.3 - - - -
165A LEU* 3.0 44.1 + - + +
166A ARG 5.3 0.2 - - - -
167A LEU* 4.4 8.5 - - + -
208A TYR* 3.6 28.3 - + - -
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Residues in contact with ARG 101 (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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100A PHE* 1.3 69.1 - - - +
102A MET* 1.3 78.0 + - - +
108A ILE* 3.0 53.7 + - + +
110A ILE* 3.5 13.8 - - + +
138A TYR* 3.4 30.3 + - + +
159A GLU* 3.0 30.6 + - - +
161A ALA 3.4 14.3 + - - -
162A GLY* 3.8 11.5 - - - -
163A THR 3.9 5.2 - - - -
164A TYR* 3.7 26.9 + - + -
195A LEU* 3.9 13.3 - - - +
197A ILE* 6.0 1.4 - - - +
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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