Contacts of the strand formed by residues 124 - 128 (chain I) 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 PHE 124 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5I ALA 3.1 12.1 - - - +
6I MET* 4.0 13.0 - - + -
110I ILE* 3.7 2.0 - - - -
122I ALA* 4.0 3.5 - - - +
123I ASP* 1.3 103.5 + - + +
125I ILE* 1.3 77.3 + - - +
126I VAL* 4.1 9.6 - - + -
135I PHE* 4.0 18.8 - + - -
138I CYS* 3.5 46.9 - - + -
139I GLU* 3.7 20.4 - - + -
142I TYR* 4.0 16.8 - + + -
165Z ARG* 3.5 33.4 + - - -
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Residues in contact with ILE 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I VAL* 3.3 4.7 - - - +
5I ALA* 2.9 31.1 + - + +
100I VAL* 3.8 25.0 - - + +
110I ILE* 3.8 14.8 - - + -
111I ALA* 3.7 19.7 - - - +
112I GLY* 3.7 21.5 - - - -
120I ASP* 3.4 44.4 - - - +
122I ALA* 3.8 11.2 - - + +
124I PHE* 1.3 83.3 - - - +
126I VAL* 1.3 72.4 + - - +
135I PHE* 6.1 0.9 - - - -
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Residues in contact with VAL 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H GLN* 5.5 3.5 + - - -
3I VAL 3.7 4.0 - - - -
4I VAL* 4.2 4.7 - - + -
100I VAL* 4.8 0.2 - - - -
120I ASP* 5.9 0.2 + - - -
124I PHE* 4.1 9.9 - - + -
125I ILE* 1.3 88.0 - - - +
127I SER* 1.3 66.6 + - - +
131I SER* 3.9 11.5 - - - +
134I LEU* 3.7 27.6 - - + -
135I PHE* 3.4 49.2 - - + +
138I CYS* 3.9 23.8 - - - -
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Residues in contact with SER 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I ILE* 3.3 8.5 - - - +
3I VAL* 2.9 31.6 + - - +
46I THR* 2.6 28.5 + - - -
98I GLY* 3.0 20.1 + - - -
99I PRO 5.3 0.2 - - - -
100I VAL* 3.8 22.4 - - - -
126I VAL* 1.3 79.1 - - - +
128I GLY* 1.3 59.9 + - - +
131I SER* 4.4 8.3 - - - -
134I LEU* 3.7 3.2 - - - +
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Residues in contact with GLY 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-5I SER 5.9 0.2 - - - -
1I GLY 3.3 13.2 - - - -
46I THR* 3.6 12.3 - - - -
127I SER* 1.3 78.8 + - - +
129I THR* 1.3 63.3 + - - -
130I ALA 3.2 3.1 - - - -
131I SER* 3.1 23.6 + - - -
201I MG 3.2 9.2 - - - -
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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