Contacts of the strand formed by residues 98 - 104 (chain B) in PDB entry 1J3R
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 GLU 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.6 7.2 - - - -
91B HIS* 3.2 17.0 - - - +
97B ALA* 1.3 78.1 - - - +
99B VAL* 1.3 72.1 + - - +
100B TYR* 3.0 27.6 - - + -
130B TYR* 4.4 0.9 - - - -
131B VAL* 2.8 46.9 + - + +
137B HIS* 3.0 21.5 + - - -
151B ALA* 3.6 5.5 - - - +
152B LEU 3.2 11.9 - - - +
153B TYR* 3.6 12.7 - - + -
601B 6PG 2.6 30.7 + - - -
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 4.1 23.8 - - + -
68A ASN 5.5 0.2 - - - +
69A PHE* 4.2 21.5 - - + -
150A LEU* 6.3 2.2 - - + -
152A LEU* 3.8 26.9 - - + -
98B GLU* 1.3 80.3 - - - +
100B TYR* 1.3 68.8 + - - +
101B PHE* 5.8 1.8 - - + -
128B ILE* 3.9 26.7 - - + -
129B VAL 3.4 4.9 - - - +
130B TYR* 4.4 11.4 - - + -
151B ALA* 3.5 1.7 - - - -
152B LEU* 2.8 41.3 + - + +
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Residues in contact with TYR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 3.0 31.4 - - + -
99B VAL* 1.3 82.0 - - - +
101B PHE* 1.3 62.9 + - - +
102B ALA 4.1 0.9 - - - +
109B MET* 3.4 28.7 - - + -
123B MET* 5.1 5.8 - - - -
127B THR 4.4 0.7 - - - -
128B ILE* 3.3 7.8 - - - +
129B VAL* 2.8 39.9 + - + +
131B VAL* 4.3 6.7 - - + -
137B HIS* 2.7 36.5 + + - -
139B THR* 3.7 8.2 + - - -
149B PHE* 3.3 43.3 - + + -
150B LEU 3.3 3.6 - - - -
151B ALA* 3.9 8.5 - - + -
152B LEU* 5.6 0.4 - - - -
601B 6PG 3.1 20.4 + - - -
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.9 19.5 - - + -
13A PHE* 3.5 27.1 - + - -
101A PHE* 3.9 27.8 - + - -
103A LEU* 4.0 5.8 - - + -
150A LEU* 3.9 20.0 - - + -
99B VAL* 5.8 1.3 - - + -
100B TYR* 1.3 74.5 - - - +
102B ALA* 1.3 66.9 + - - +
103B LEU* 3.5 25.2 + - + +
126B GLY* 3.5 28.7 - - - -
127B THR 3.5 6.5 - - - -
128B ILE* 3.5 22.2 - - + -
149B PHE* 3.4 2.2 - - - -
150B LEU* 2.8 45.0 + - + +
152B LEU* 5.3 4.0 - - + -
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 4.2 0.2 - - - -
100B TYR* 5.4 0.6 - - - +
101B PHE* 1.3 75.2 - - - +
103B LEU* 1.3 64.5 + - - +
104B LYS 5.2 0.2 - - - +
123B MET* 4.2 16.9 - - + -
124B GLU 3.2 28.9 - - - +
125B PRO* 4.1 0.7 - - + -
126B GLY 3.0 24.1 + - - -
127B THR* 2.9 17.4 + - - +
147B PHE* 4.4 11.9 - - + -
148B ILE 3.9 0.2 - - - -
149B PHE* 3.9 10.3 - - + +
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Residues in contact with LEU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 4.4 11.1 - - + -
101A PHE* 4.0 8.3 - - + -
11B LEU* 3.9 40.2 - - + -
13B PHE* 4.4 24.1 - - + +
71B THR* 4.8 3.1 - - + -
101B PHE* 3.6 37.7 - - + +
102B ALA* 1.3 80.4 - - - +
104B LYS* 1.3 61.9 + - + +
125B PRO* 3.7 15.6 - - - +
148B ILE* 2.7 25.2 + - + +
149B PHE 4.6 1.8 - - - -
150B LEU* 4.2 16.6 - - + +
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B PHE 3.9 12.6 - - - +
14B GLU* 3.0 52.2 + - - +
102B ALA* 5.2 0.4 - - - +
103B LEU* 1.3 81.8 - - - +
105B GLY* 1.3 70.3 + - - +
125B PRO* 3.9 6.2 - - - +
146B PRO* 4.0 6.7 - - + +
147B PHE* 3.3 6.2 - - - -
148B ILE* 2.8 46.7 + - + +
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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