Contacts of the strand formed by residues 86 - 92 (chain D) in PDB entry 5JCZ
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 GLY 86 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13D LYS 3.4 5.7 + - - +
14D VAL* 3.3 12.0 - - - -
15D VAL* 3.0 24.1 + - - +
84D ALA* 3.5 1.9 - - - +
85D VAL* 1.3 81.9 - - - +
87D ALA* 1.3 62.6 + - - +
117D ILE* 3.5 6.3 - - - +
118D VAL 3.3 9.9 - - - -
168D ILE* 4.3 3.1 - - - -
172D ILE* 3.7 14.1 - - - -
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Residues in contact with ALA 87 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D VAL* 4.3 0.7 - - - -
15D VAL* 3.3 23.3 - - + +
17D ILE* 4.8 6.5 - - + -
86D GLY* 1.3 75.7 - - - +
88D LEU* 1.3 59.8 + - - +
89D LEU 3.9 0.6 + - - -
109D LEU* 4.4 21.3 - - + -
117D ILE* 3.9 13.0 - - + -
118D VAL 2.8 8.3 + - - +
119D ILE* 3.5 5.3 - - + +
120D MET 3.0 24.8 + - - -
168D ILE* 3.5 9.1 - - - +
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Residues in contact with LEU 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D VAL* 4.7 4.9 - - + -
15D VAL 3.0 7.1 + - - -
16D LEU* 3.9 18.2 - - + -
17D ILE* 3.1 30.9 + - - +
27D LEU* 5.1 9.2 - - + -
87D ALA* 1.3 71.4 - - - +
89D LEU* 1.3 61.7 + - - +
90D VAL* 3.5 10.2 + - + +
120D MET* 3.5 32.1 - - + -
122D VAL* 4.0 16.8 - - + -
164D ALA* 4.8 6.5 - - + +
165D PHE* 3.5 43.3 - - + -
168D ILE* 3.8 19.5 - - + -
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Residues in contact with LEU 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D ILE* 3.7 22.7 - - + +
87D ALA 3.9 1.6 + - - -
88D LEU* 1.3 68.5 - - - +
90D VAL* 1.3 62.0 + - - +
102D VAL* 3.8 39.3 - - + -
105D TRP* 3.8 25.1 - - + -
106D LEU* 4.1 33.9 - - + -
119D ILE* 4.3 16.4 - - + -
120D MET 2.8 14.5 + - - +
121D LEU* 3.4 13.8 - - + +
122D VAL 2.7 27.6 + - - -
148D LEU* 4.7 7.2 - - + -
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Residues in contact with VAL 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D LEU* 5.4 2.7 - - + -
17D ILE 2.9 14.4 + - - +
18D GLY* 3.4 19.8 - - - -
19D ASP 4.1 1.0 + - - -
22D VAL* 3.7 26.4 - - + +
24D LYS* 4.2 10.8 - - + -
27D LEU* 3.9 24.0 - - + -
88D LEU* 3.7 20.0 - - + +
89D LEU* 1.3 79.8 - - - +
91D TYR* 1.3 71.4 + - - +
98D THR 4.9 1.7 - - - +
102D VAL* 5.0 0.7 - - - +
105D TRP* 5.4 0.3 - - - -
122D VAL* 3.2 17.0 - - + +
124D ASN* 3.8 17.9 - - + -
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Residues in contact with TYR 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D VAL* 3.9 11.7 - - - -
90D VAL* 1.3 73.3 - - - +
92D ASP* 1.3 71.6 + - - +
93D ILE* 3.9 14.2 - - + +
98D THR* 3.5 25.1 - - - +
99D TYR* 3.9 27.1 - + + -
102D VAL* 4.0 3.4 - - + -
121D LEU* 3.7 34.1 - - + -
122D VAL 2.9 13.0 + - - -
123D GLY* 3.4 24.8 - - - -
124D ASN* 2.9 30.8 + - - +
134D VAL* 3.7 20.8 + - + +
136D THR* 5.7 0.2 - - - -
139D ALA* 3.1 22.7 - - + +
150D PHE* 3.4 11.5 - + - -
152D GLU* 4.6 3.1 + - - -
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Residues in contact with ASP 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D GLY 4.4 1.1 - - - +
22D VAL* 3.8 12.5 - - + +
91D TYR* 1.3 77.3 - - - +
93D ILE* 1.3 59.2 + - - +
94D ALA* 2.8 29.6 + - - +
95D LYS* 2.9 57.0 + - + +
98D THR* 2.8 22.8 + - + +
124D ASN 4.0 3.4 - - - -
125D LYS* 3.0 43.8 + - - +
128D LEU* 5.2 0.7 - - - +
134D VAL* 4.0 0.7 - - - +
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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