Contacts of the strand formed by residues 173 - 179 (chain J) in PDB entry 3SDI
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 VAL 173 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2J ILE* 4.8 8.3 - - + -
4J LEU* 5.3 0.2 - - + -
15J ALA* 4.0 11.0 - - + -
16J SER* 3.3 31.0 - - - +
17J SER* 3.9 4.9 - - - +
18J LYS* 3.8 13.0 - - - +
159J VAL* 3.8 32.0 - - + +
170J PHE* 4.3 9.0 - - + -
172J GLY* 1.3 76.6 - - - +
174J ILE* 1.3 61.1 + - - +
175J VAL* 3.8 23.2 + - + +
190J PHE* 3.9 20.3 - - + +
191J GLN* 6.1 0.7 - - - -
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Residues in contact with ILE 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14J LEU 3.6 1.7 - - - +
15J ALA* 3.4 3.5 - - - -
16J SER* 3.0 33.9 + - - +
18J LYS* 3.7 25.3 - - + +
30J SER* 4.5 5.4 - - - +
31J ASP 3.7 24.2 - - - +
32J ASP* 4.0 24.7 - - + +
173J VAL* 1.3 72.1 - - - +
175J VAL* 1.3 61.6 + - - +
176J LYS* 4.2 20.8 + - + +
186J GLN* 3.9 29.8 - - - +
187J VAL 5.6 0.9 - - - -
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Residues in contact with VAL 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13J ILE* 3.6 27.8 - - + -
14J LEU 3.3 4.9 - - - +
15J ALA* 4.3 6.3 - - + -
152J LEU* 3.8 19.1 - - + -
155J LEU* 4.4 1.6 - - + -
173J VAL* 3.8 16.8 + - + -
174J ILE* 1.3 75.3 - - - +
176J LYS* 1.3 70.9 + - - +
186J GLN* 3.6 4.7 - - - +
187J VAL* 3.1 43.4 + - + +
190J PHE* 3.6 37.2 - - + +
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Residues in contact with LYS 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12J VAL 3.9 0.7 - - - +
13J ILE* 3.5 3.3 - - - +
14J LEU* 2.9 37.1 + - + +
32J ASP* 2.8 30.8 + - - -
34J THR* 2.9 32.3 - - + +
42J LEU* 3.5 29.1 - - + +
174J ILE* 4.2 10.5 - - + +
175J VAL* 1.3 81.0 - - - +
177J ILE* 1.3 63.8 + - - +
184J ILE* 4.7 10.1 - - + -
185J ARG 3.4 7.9 - - - +
186J GLN* 3.7 28.8 - - + +
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Residues in contact with ILE 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J SER* 3.9 25.6 - - - +
12J VAL 3.7 4.9 - - - +
13J ILE* 4.5 11.7 - - + -
148J THR* 3.7 16.4 - - + +
152J LEU* 4.1 14.8 - - + -
176J LYS* 1.3 76.6 - - - +
178J VAL* 1.3 67.4 + - - +
179J ASP 4.1 0.4 - - - +
183J GLY 3.7 0.9 - - - +
184J ILE* 3.4 4.9 - - - +
185J ARG* 2.8 78.0 + - + +
187J VAL* 3.6 28.0 - - + -
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Residues in contact with VAL 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J SER* 3.2 3.9 - - - -
12J VAL* 3.0 41.6 + - + +
14J LEU* 5.5 1.3 - - + -
40J HIS* 3.6 31.9 - - - +
41J THR 4.6 0.2 - - - +
42J LEU* 3.7 38.8 - - + -
102J GLY* 4.2 6.7 - - - +
103J GLY* 4.0 6.3 - - - -
104J TYR* 3.7 16.3 - - + +
108J PRO* 5.2 0.2 - - - +
176J LYS 4.9 0.2 - - - +
177J ILE* 1.3 78.4 - - - +
179J ASP* 1.3 61.7 + - - +
183J GLY 3.4 4.7 - - - +
184J ILE* 3.9 11.2 - - + -
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Residues in contact with ASP 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10J ASP 3.4 21.8 - - - +
11J SER* 3.7 8.3 - - - -
40J HIS* 3.7 3.5 - - - -
104J TYR* 3.6 18.3 - - - +
148J THR* 5.6 1.3 + - - +
177J ILE* 4.9 0.2 - - - +
178J VAL* 1.3 75.5 - - - +
180J LYS* 1.3 69.0 + - + +
181J ASP* 3.1 24.8 + - - +
183J GLY* 3.0 24.3 + - - +
185J ARG* 2.7 33.4 + - - -
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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