Contacts of the strand formed by residues 104 - 109 (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 ARG 104 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2144A A 5.6 1.2 - - - -
2145A G 2.9 49.6 + - - +
2146A A 5.0 4.0 - - - -
2147A G 3.2 42.8 - - - +
2256A U 4.1 12.1 + - - -
100R LYS* 5.0 2.2 - - - +
100S HIS* 3.5 4.0 - - - -
101S PHE 3.1 16.7 + - - +
102S ALA* 3.1 37.2 + - - +
103S SER* 1.3 81.3 - - - +
105S GLN* 1.3 63.5 + - - +
106S TRP* 3.1 49.4 + - + +
115S LEU 5.6 0.2 + - - -
116S ILE* 4.2 8.5 - - - +
117S GLY* 4.3 14.5 + - - +
118S ASN* 5.6 0.4 + - - -
118b PRO* 6.0 0.7 - - - -
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Residues in contact with GLN 105 (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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2147A G 4.9 7.9 + - - +
96R GLU 3.1 17.6 + - - -
97R LEU* 3.3 7.8 - - - +
98R ASN* 2.7 49.4 + - + +
100R LYS* 3.2 22.7 + - - -
101R VAL* 3.3 16.6 - - + +
98S VAL* 4.0 4.7 - - + +
99S VAL 3.4 8.1 - - - +
100S HIS* 3.8 21.7 + - + -
103S SER 5.6 0.2 - - - +
104S ARG* 1.3 76.0 - - - +
106S TRP* 1.3 62.2 + - - +
134S LEU* 3.9 24.7 - - + +
43j LEU* 4.8 6.5 - - - +
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Residues in contact with TRP 106 (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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100R LYS* 4.5 8.7 - - - +
101R VAL* 4.0 0.2 - - - +
98S VAL* 3.2 5.1 - - - +
99S VAL* 2.9 35.4 + - + +
101S PHE* 3.0 35.8 + - + +
104S ARG* 3.1 53.2 + - + +
105S GLN* 1.3 75.5 - - - +
107S LYS* 1.3 59.6 + - - +
108S VAL* 3.1 19.8 - - + +
114S ILE* 3.6 40.8 - - + -
115S LEU 3.3 21.1 - - - -
116S ILE* 4.5 9.6 - - + -
118b PRO* 3.6 26.9 - - + -
119b PHE* 4.3 15.7 - + - -
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Residues in contact with LYS 107 (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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100R LYS* 6.1 0.4 - - - +
101R VAL* 4.3 9.1 - - + +
104R ASP* 4.3 19.5 + - + +
105R LEU* 5.5 1.6 - - + -
108R TYR* 3.3 25.3 - - + +
109R GLU* 2.8 37.5 + - - +
96S PHE* 5.3 3.6 - - + -
97S ALA 3.5 4.9 - - - +
98S VAL* 4.2 17.0 - - + +
106S TRP* 1.3 71.5 - - - +
108S VAL* 1.3 59.4 + - - +
109S THR* 5.8 3.8 - - + -
112S ASP* 4.1 6.2 - - - +
114S ILE* 5.1 1.2 - - - +
212T LEU* 3.3 46.5 - - + +
119b PHE* 6.0 1.9 - - - +
121b THR* 4.9 7.1 - - - +
124b PRO* 2.8 23.9 + - - -
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Residues in contact with VAL 108 (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* 3.3 5.4 - - - +
97S ALA* 2.8 37.1 + - + +
99S VAL* 3.9 17.9 - - + -
106S TRP* 3.1 23.1 - - + +
107S LYS* 1.3 75.7 - - - +
109S THR* 1.3 63.4 + - - +
112S ASP* 3.1 32.3 - - - +
114S ILE* 3.6 19.1 - - + -
130S LEU* 6.1 0.9 - - + -
156S VAL* 5.6 0.9 - - + -
195S ILE* 3.3 33.0 - - + -
198S ILE* 3.7 3.4 - - + +
121b THR* 5.8 0.7 - - - -
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Residues in contact with THR 109 (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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109R GLU* 5.4 0.2 - - - +
94S ARG* 4.2 8.6 + - - -
95S LEU 3.7 7.0 - - - +
96S PHE* 3.7 5.6 - - + -
107S LYS* 5.7 4.5 - - - +
108S VAL* 1.3 81.9 - - - +
110S SER* 1.3 74.0 + - - +
112S ASP* 3.2 31.9 + - - +
195S ILE* 3.4 12.1 - - - +
198S ILE* 4.1 7.0 - - - -
121b THR* 4.6 7.4 - - + +
123b ASN 4.1 16.4 + - - +
124b PRO* 4.8 4.9 - - + +
126b ILE* 3.6 30.5 - - + -
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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