Contacts of the strand formed by residues 133 - 137 (chain A) in PDB entry 1JTF
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 ILE 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A THR* 3.4 4.3 - - - +
65A VAL* 3.5 24.2 - - + -
125A LYS* 4.0 18.8 - - + +
128A LEU* 3.8 34.1 - - + -
131A SER 3.7 9.4 - - - +
132A LYS* 1.3 77.4 - - - +
134A ILE* 1.3 73.5 + - - +
135A LEU* 4.1 5.8 - - + +
167A LEU* 3.6 33.9 - - + +
168A ASN 5.3 1.8 + - - -
169A PRO* 3.3 16.2 - - + +
170A VAL* 2.8 36.4 + - - +
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Residues in contact with ILE 134 (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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49A PHE* 3.8 20.6 - - + -
50A LEU* 4.4 5.6 - - + -
53A LEU* 3.3 37.2 - - + -
58A ILE 4.0 2.9 - - - +
59A LEU* 3.7 26.2 - - + -
62A ALA* 3.6 26.5 - - + -
63A THR 2.9 8.8 + - - +
64A VAL* 3.3 12.8 - - + +
65A VAL 2.8 26.0 + - - +
133A ILE* 1.3 79.7 - - - +
135A LEU* 1.3 63.7 + - - +
136A ILE* 4.7 2.5 - - + -
170A VAL* 3.9 12.6 - - + -
171A ALA* 3.8 6.3 - - + +
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Residues in contact with LEU 135 (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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49A PHE* 4.2 1.4 - - - -
65A VAL* 3.4 14.1 - - + +
67A ILE* 3.5 26.9 - - + -
133A ILE* 4.0 5.8 - - + -
134A ILE* 1.3 73.1 - - - +
136A ILE* 1.3 88.6 + - - +
137A SER* 4.5 1.6 - - - +
163A MET* 3.5 35.2 - - + +
164A ILE* 4.3 20.0 - - + +
167A LEU* 4.5 6.3 - - + -
169A PRO* 4.3 13.9 - - + -
171A ALA 3.3 8.4 + - - +
172A SER* 3.1 7.3 - - - -
173A SER 2.9 26.0 + - - -
174A LEU* 4.4 9.4 - - + -
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Residues in contact with ILE 136 (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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46A GLU* 4.3 18.6 - - + +
49A PHE* 4.2 20.6 - - + -
50A LEU* 4.2 23.6 - - + -
64A VAL* 3.8 25.4 - - + -
65A VAL 2.8 6.1 + - - +
66A TYR* 3.1 42.8 - - + -
67A ILE 2.7 29.6 + - - -
91A TRP* 4.9 2.0 - - + -
134A ILE* 4.7 1.1 - - + -
135A LEU* 1.3 85.0 - - - +
137A SER* 1.3 60.6 + - - +
138A ASP* 5.6 0.7 - - + -
173A SER* 3.4 15.5 - - - +
209A ARG* 5.9 2.0 - - - +
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Residues in contact with SER 137 (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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67A ILE* 3.2 7.9 - - - -
135A LEU* 4.5 1.6 - - - -
136A ILE* 1.3 78.1 - - - +
138A ASP* 1.3 63.7 + - - +
139A VAL* 4.0 3.8 - - - +
160A GLN* 2.7 33.4 + - - +
163A MET* 3.7 24.9 - - - +
173A SER 3.2 7.5 + - - +
174A LEU* 3.6 20.6 - - - -
175A LYS 3.6 11.4 + - - -
209A ARG* 3.5 12.1 + - - -
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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