Contacts of the strand formed by residues 96 - 101 (chain S) in PDB entry 3J7Y
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 96 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105R LEU* 4.5 3.1 - - + -
109R GLU* 3.0 46.4 - - + +
112R THR* 3.5 11.2 - - + -
95S LEU* 1.3 73.9 - - - +
97S ALA* 1.3 68.6 + - - +
98S VAL* 5.0 3.4 - - + -
107S LYS* 5.3 3.1 - - + -
108S VAL 3.3 14.6 - - - +
109S THR* 3.7 12.1 - - + -
135S LEU* 3.6 17.7 - - + -
136S VAL* 3.3 7.3 - - - +
137S GLY* 2.8 59.7 + - - +
138S ALA* 3.9 1.6 - - - -
198S ILE* 3.8 3.6 - - - -
126b ILE* 3.6 19.3 - - + -
127b GLN* 3.3 29.4 - - - -
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Residues in contact with ALA 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96S PHE* 1.3 77.3 - - - +
98S VAL* 1.3 62.3 + - - +
99S VAL* 3.7 18.6 - - + -
106S TRP 3.2 3.1 - - - +
107S LYS* 4.3 0.4 - - - -
108S VAL* 2.8 42.2 + - + +
133S VAL* 4.1 5.4 - - + -
135S LEU 3.2 11.2 - - - +
136S VAL* 4.3 6.3 - - + -
156S VAL* 3.9 17.3 - - + -
198S ILE* 4.0 8.5 - - + -
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Residues in contact with VAL 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R LEU* 4.3 1.3 - - + -
101R VAL* 3.6 46.9 - - + -
105R LEU* 5.0 8.1 - - + -
96S PHE* 5.0 3.1 - - + -
97S ALA* 1.3 71.0 - - - +
99S VAL* 1.3 59.1 + - - +
105S GLN* 4.0 8.5 - - + -
106S TRP 3.2 5.8 - - - +
107S LYS* 4.2 13.0 - - + -
133S VAL* 3.7 0.6 - - - -
134S LEU* 3.1 47.6 + - + +
135S LEU* 2.8 39.3 + - + +
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Residues in contact with VAL 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97S ALA* 3.7 18.6 - - + +
98S VAL* 1.3 75.6 - - - +
100S HIS* 1.3 68.8 + - - +
101S PHE* 4.0 2.0 - - + +
105S GLN* 3.4 6.3 - - - +
106S TRP* 2.9 32.3 + - + -
108S VAL* 3.9 17.0 - - + -
130S LEU* 3.8 28.3 - - + -
131S GLU 3.6 20.0 - - - +
132S LYS 3.5 5.2 - - - +
133S VAL* 3.6 21.8 - - + +
134S LEU* 5.1 0.2 - - - -
156S VAL* 4.0 12.1 - - + -
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Residues in contact with HIS 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2255A C 5.0 1.5 + - - -
2256A U 6.2 0.9 - - - -
99S VAL* 1.3 75.0 - - - +
101S PHE* 1.3 61.4 + - - +
103S SER* 3.7 34.2 + - - -
104S ARG 3.5 6.1 - - - -
105S GLN* 3.8 26.4 + - + +
131S GLU 4.0 10.6 - - - +
132S LYS* 3.0 32.6 + - + +
134S LEU* 4.7 7.0 - - + -
148S LEU* 5.4 0.2 - - + -
43j LEU* 3.2 41.9 - - + +
44j THR* 4.9 8.3 - - + +
48j ASP* 3.4 27.3 + - - +
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Residues in contact with PHE 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99S VAL* 5.4 3.1 - - + -
100S HIS* 1.3 73.9 + - - +
102S ALA* 1.3 87.0 + - + +
103S SER 3.3 1.6 - - - -
104S ARG* 3.1 10.7 + - - +
106S TRP* 3.0 32.8 + - + +
114S ILE* 6.1 1.6 - - + -
116S ILE* 3.6 23.1 - - + -
120S LEU* 3.5 37.9 - - + -
122S LEU* 6.2 0.2 - - + -
128S ILE* 5.0 2.9 - - + -
130S LEU* 3.5 35.4 - - + -
193S LEU* 3.5 21.5 - - + -
48j ASP* 4.5 9.2 - - + -
49j TRP* 4.0 27.6 - + + -
60j MET* 6.5 0.4 - - - -
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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