Contacts of the strand formed by residues 98 - 104 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91A HIS* 3.1 9.7 + - + +
97A ALA* 1.3 77.5 - - - +
99A VAL* 1.3 71.6 + - - +
100A TYR* 3.3 29.7 - - + -
130A TYR* 3.9 1.0 - - - -
131A VAL* 2.8 42.8 + - + +
137A HIS* 3.0 16.6 + - - -
151A ALA* 3.3 12.5 - - - +
152A LEU 3.4 14.8 - - - +
153A TYR* 3.5 9.3 - - + -
201A FE 2.9 21.0 - - - -
600A 6PG 2.7 23.1 + - - -
67B LEU* 3.7 2.2 - - - +
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Residues in contact with VAL 99 (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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98A GLU* 1.3 80.5 - - - +
100A TYR* 1.3 69.6 + - - +
101A PHE* 5.7 1.1 - - + -
128A ILE* 3.8 27.6 - - + -
129A VAL 3.4 4.9 - - - +
130A TYR* 4.4 11.7 - - + -
150A LEU 3.8 0.3 - - - +
151A ALA* 3.3 2.9 - - - -
152A LEU* 2.8 41.6 + - + +
67B LEU* 4.1 23.3 - - + -
68B ASN 5.6 0.2 - - - +
69B PHE* 4.2 20.2 - - + -
150B LEU* 6.2 0.9 - - + -
152B LEU* 3.7 28.7 - - + -
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Residues in contact with TYR 100 (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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89A HIS* 5.0 0.2 - - - -
98A GLU* 3.3 31.4 - - + -
99A VAL* 1.3 81.4 - - - +
101A PHE* 1.3 60.6 + - - +
102A ALA 4.1 0.2 - - - -
109A MET* 3.3 28.7 - - + -
123A MET* 4.1 13.0 - - + -
127A THR 4.4 0.2 - - - -
128A ILE* 3.1 10.3 - - - +
129A VAL* 2.8 33.6 + - + +
131A VAL* 4.1 6.1 - - + -
137A HIS* 2.9 34.1 + + - -
139A THR* 3.5 16.4 + - - -
149A PHE* 3.2 41.3 - + - -
150A LEU 3.3 2.7 - - - -
151A ALA* 4.0 6.5 - - + -
600A 6PG 3.5 18.4 + - - -
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Residues in contact with PHE 101 (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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99A VAL* 5.7 1.8 - - + -
100A TYR* 1.3 75.5 - - - +
102A ALA* 1.3 65.0 + - - +
103A LEU* 3.6 23.1 + - + +
126A GLY* 3.7 28.0 - - - -
127A THR 3.4 5.8 - - - -
128A ILE* 3.6 16.8 - - + -
149A PHE* 3.4 1.9 - - - -
150A LEU* 2.7 49.3 + - + +
152A LEU* 5.4 3.6 - - + -
11B LEU* 3.8 24.5 - - + -
13B PHE* 3.4 23.6 - + - -
101B PHE* 3.9 25.6 - + - -
103B LEU* 4.0 8.7 - - + -
150B LEU* 3.9 23.3 - - + -
152B LEU* 6.2 0.2 - - + -
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Residues in contact with ALA 102 (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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100A TYR 4.1 0.4 - - - -
101A PHE* 1.3 74.8 - - - +
103A LEU* 1.3 65.0 + - - +
104A LYS 5.2 0.4 - - - +
123A MET* 4.0 22.7 - - + +
124A GLU 3.2 26.7 - - - +
125A PRO* 4.2 0.4 - - - -
126A GLY* 3.0 24.6 + - - -
127A THR 2.9 13.3 + - - +
147A PHE* 4.2 15.0 - - + -
149A PHE* 3.8 10.0 - - - +
13B PHE* 4.1 0.2 - - - -
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Residues in contact with LEU 103 (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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11A LEU* 3.9 38.4 - - + -
13A PHE* 4.2 26.5 - - + +
71A THR* 4.9 0.7 - - + -
101A PHE* 3.7 35.4 - - + +
102A ALA* 1.3 81.8 - - - +
104A LYS* 1.3 62.0 + - + +
125A PRO* 3.9 14.8 - - - +
148A ILE* 2.8 26.4 + - + +
149A PHE 4.6 2.7 - - - -
150A LEU* 4.3 15.3 - - + +
13B PHE* 4.3 11.6 - - + -
101B PHE* 4.0 9.6 - - + -
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Residues in contact with LYS 104 (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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13A PHE 4.2 10.3 - - - +
14A GLU* 3.0 42.0 + - - +
102A ALA* 3.9 0.6 - - - +
103A LEU* 1.3 81.0 - - - +
105A GLY* 1.3 69.8 + - - +
125A PRO* 4.0 6.2 - - - +
145A LYS* 6.4 2.2 - - + -
146A PRO* 3.9 9.6 - - + +
147A PHE* 3.3 6.5 - - - -
148A ILE* 2.7 62.8 + - + -
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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