Contacts of the strand formed by residues 296 - 301 (chain E) 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 LEU 296 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100E ILE* 4.0 11.4 - - + +
101E ALA 3.4 5.6 - - - +
102E LEU* 3.4 30.1 - - + -
150E LYS* 3.9 25.6 - - + +
174E GLN* 3.5 34.8 - - + +
175E THR* 3.1 42.8 - - + +
177E LYS* 4.5 11.8 + - - +
208E ALA* 4.0 4.9 - - - +
209E LYS 5.1 0.3 + - - -
294E ASN 4.2 3.6 - - - +
295E CYS* 1.3 88.5 - - - +
297E VAL* 1.3 58.8 + - - +
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Residues in contact with VAL 297 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ILE* 3.3 8.8 - - - +
101E ALA 2.7 41.7 + - - +
103E LYS* 4.3 7.6 - - + -
122E LEU* 3.7 25.1 - - + -
177E LYS* 5.2 2.9 - - - +
206E VAL* 3.7 15.3 - - + -
207E THR 3.4 10.8 - - - +
208E ALA* 3.4 22.2 - - + -
289E VAL* 3.7 16.8 - - + -
290E PRO 4.1 3.8 - - - +
295E CYS* 4.1 9.9 - - - +
296E LEU* 1.3 76.5 - - - +
298E LYS* 1.3 57.5 + - - +
299E VAL* 3.8 10.3 - - + -
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Residues in contact with LYS 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3204A C 2.7 37.8 + - - +
3205A C 3.1 25.0 + - - +
99E LEU 3.5 4.5 - - - +
100E ILE* 4.5 2.9 - - + +
177E LYS* 4.0 27.5 - - + +
178E ILE 3.6 17.3 + - - -
179E PHE* 3.3 41.2 - - + +
205E ASP 3.6 1.4 - - - +
206E VAL* 3.3 6.8 - - - +
207E THR* 2.9 49.5 + - + +
297E VAL* 1.3 73.3 - - - +
299E VAL* 1.3 62.2 + - - +
300E LYS* 4.2 4.0 - - + -
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Residues in contact with VAL 299 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98E GLY* 3.2 4.9 - - - -
99E LEU* 2.8 45.8 + - + +
101E ALA* 4.2 13.2 - - + -
122E LEU* 3.7 27.8 - - + -
124E VAL* 6.3 0.2 - - + -
179E PHE* 4.0 1.0 - - - -
198E PHE* 3.5 25.2 - - + -
204E VAL* 3.3 27.4 - - + -
205E ASP 3.6 2.5 - - - -
206E VAL* 4.4 4.7 - - + +
283E ILE* 5.5 6.3 - - + -
285E VAL* 5.5 2.7 - - + -
297E VAL* 3.8 12.1 - - + -
298E LYS* 1.3 78.1 - - - +
300E LYS* 1.3 60.3 + - - +
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Residues in contact with LYS 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3203A A 4.1 11.0 - - - +
3204A C 3.3 39.7 + - - +
95E PHE* 5.6 8.1 - - - +
96E ARG 5.1 7.4 + - - +
97E VAL 5.8 0.2 - - - -
98E GLY* 4.4 4.0 - - - +
179E PHE* 3.9 21.1 - - + +
180E ASN 5.0 10.1 + - - +
198E PHE* 4.1 6.5 - - - -
204E VAL* 3.1 9.2 - - - +
205E ASP* 2.8 57.3 + - + +
207E THR* 5.5 1.8 - - + -
298E LYS* 4.4 10.5 - - + +
299E VAL* 1.3 76.4 - - - +
301E ASP* 1.3 74.2 + - - +
303E LYS* 6.0 2.0 - - - -
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Residues in contact with ASP 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E SER 5.7 0.2 - - - +
95E PHE* 4.7 18.0 - - - -
96E ARG* 4.9 17.0 + - + +
97E VAL 5.5 2.6 + - - +
198E PHE* 4.0 6.7 - - + -
202E GLN* 3.8 22.3 + - - +
203E TYR 3.9 8.6 - - - +
205E ASP* 4.2 0.3 - - - +
300E LYS* 1.3 95.4 + - - +
302E SER* 1.3 91.8 + - - +
307E TYR 4.6 6.4 - - - +
308E LYS 5.7 0.7 - - - +
310E LEU* 4.8 8.1 - - - +
314E LEU* 5.8 2.2 - - - -
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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