Contacts of the strand formed by residues 67 - 74 (chain B) in PDB entry 1J3Q
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 LEU 67 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A LEU* 3.9 27.4 - - + -
97A ALA* 3.7 11.9 - - + +
98A GLU* 3.6 34.5 - - - +
99A VAL* 4.0 17.0 - - + +
130A TYR* 4.0 7.9 - - + -
152A LEU* 3.7 15.5 - - + +
153A TYR* 4.3 1.3 - - - -
154A PRO* 4.1 15.3 - - + -
58B ILE 4.9 0.3 - - - +
60B GLN* 3.3 22.2 + - - +
66B ASP* 1.3 94.3 + - - +
68B ASN* 1.3 64.0 + - - +
69B PHE* 4.9 2.3 - - - -
152B LEU* 5.9 4.0 - - + -
153B TYR* 3.8 14.1 - - - +
154B PRO* 4.2 3.8 - - + -
155B ALA 4.0 0.7 - - - +
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Residues in contact with ASN 68 (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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58B ILE 3.8 3.8 - - - -
59B GLU* 3.6 23.2 + - + +
60B GLN* 2.5 35.4 + - - +
67B LEU* 1.3 81.1 - - - +
69B PHE* 1.3 65.4 + - - +
152B LEU* 3.6 2.8 - - - +
153B TYR* 3.0 63.4 + - + +
154B PRO 4.3 0.2 + - - -
155B ALA* 3.4 29.1 + - - +
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 4.0 24.2 - - + -
128A ILE* 3.8 41.5 - - + -
130A TYR* 4.6 16.8 - + + -
7B PHE* 4.4 8.7 - + - -
9B VAL* 4.4 3.4 - - + -
18B ILE* 4.3 11.0 - - + -
57B ALA* 4.2 0.2 - - - +
58B ILE* 3.0 77.2 + - + +
60B GLN* 5.5 0.7 - - - -
67B LEU 4.9 2.2 - - - -
68B ASN* 1.3 80.6 - - - +
70B ALA* 1.3 65.1 + - - +
150B LEU* 4.5 3.8 - - + -
151B ALA 3.2 11.0 - - - +
152B LEU* 3.8 17.3 - - + -
153B TYR* 4.3 4.1 + - - -
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Residues in contact with ALA 70 (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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18B ILE* 4.4 4.0 - - - -
55B VAL* 3.9 11.7 - - + -
56B TYR 3.2 16.2 - - - +
57B ALA* 3.5 17.7 - - + -
69B PHE* 1.3 79.8 - - - +
71B THR* 1.3 62.5 + - - +
72B THR* 5.0 1.4 + - - +
149B PHE* 4.0 0.3 - - - +
150B LEU* 3.5 6.2 - - - +
151B ALA* 2.8 41.2 + - + +
153B TYR* 4.4 12.3 - - + +
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Residues in contact with THR 71 (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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11B LEU* 3.8 20.4 - - + -
16B GLY* 2.7 33.7 + - - +
18B ILE* 3.6 16.3 - - + +
54B GLU 4.0 0.4 - - - +
55B VAL* 3.3 6.4 - - - +
56B TYR* 2.9 47.4 + - - +
70B ALA* 1.3 74.8 - - - +
72B THR* 1.3 63.8 + - - +
73B VAL* 5.8 0.4 - - - -
103B LEU* 4.7 4.5 - - + -
148B ILE* 5.0 1.6 - - + -
149B PHE 3.1 12.6 - - - +
150B LEU* 4.0 9.4 - - + -
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Residues in contact with THR 72 (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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53B TYR* 4.1 24.7 - - + -
54B GLU 3.3 9.0 - - - +
55B VAL* 4.0 12.4 - - + +
70B ALA* 5.0 1.9 + - - +
71B THR* 1.3 77.7 + - - +
73B VAL* 1.3 74.2 + - - +
74B LEU* 4.2 2.5 - - + +
86B THR* 4.6 7.2 - - + -
147B PHE 3.7 1.4 - - - +
148B ILE* 3.5 7.4 - - - +
149B PHE* 3.0 63.0 + - + -
151B ALA* 5.8 1.4 - - - +
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Residues in contact with VAL 73 (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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15B THR 3.8 21.5 - - - +
16B GLY* 5.0 1.3 - - - -
53B TYR* 3.1 5.4 - - - -
54B GLU* 2.7 40.4 + - - +
56B TYR* 4.0 24.7 - - + -
71B THR 5.6 0.4 - - - -
72B THR* 1.3 76.1 - - - +
74B LEU* 1.3 60.2 + - - +
75B TYR* 3.6 33.3 + - + +
146B PRO* 4.5 9.6 - - + -
147B PHE 3.8 2.0 - - - -
148B ILE* 4.4 20.2 - - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 3.6 11.4 - - + +
53B TYR* 3.6 23.3 - - + -
72B THR* 3.8 2.4 - - + -
73B VAL* 1.3 70.9 - - - +
75B TYR* 1.3 55.7 + - - +
84B PHE 4.0 2.7 - - - +
85B MET* 4.0 23.1 - - - +
86B THR* 4.2 4.7 - - + -
139B THR* 3.6 37.9 - - + +
140B ILE 3.7 0.7 - - - -
141B ASN* 2.6 61.7 + - + +
146B PRO* 4.6 0.9 - - - -
147B PHE* 2.9 31.8 + - + +
149B PHE* 4.5 7.0 - - + -
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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