Contacts of the strand formed by residues 311 - 320 (chain E) in PDB entry 5LK5
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 PHE 311 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81E PHE* 3.4 11.4 - - + -
83E PRO* 3.0 23.9 - - - +
84E PHE* 2.7 51.7 + + + +
85E SER* 4.7 0.4 - - - -
86E ASN* 3.4 30.7 - - + -
91E LEU* 3.9 19.5 - - + -
112E LEU* 3.8 29.8 - - + -
113E PHE 3.6 4.7 - - - +
129E ASN* 3.4 31.2 - - + -
130E ILE* 3.9 5.6 - - + -
308E TYR* 3.6 27.4 - + + -
310E ASN* 1.3 77.1 - - - +
312E GLY* 1.3 57.0 + - - +
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Residues in contact with GLY 312 (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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80E SER* 3.2 6.6 - - - -
81E PHE* 3.0 41.3 + - - +
83E PRO* 4.4 0.9 - - - -
113E PHE 2.9 7.2 + - - -
115E ASN* 3.7 23.7 - - - +
310E ASN* 3.5 2.4 + - - -
311E PHE* 1.3 73.9 - - - +
313E VAL* 1.3 67.4 + - - +
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Residues in contact with VAL 313 (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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78E SER* 3.4 33.9 - - - +
79E ALA 3.4 9.6 - - - +
80E SER* 4.1 6.1 - - - -
81E PHE* 3.6 6.7 - - - -
111E LYS 3.7 0.5 - - - +
112E LEU* 3.5 4.0 - - - +
113E PHE* 2.7 45.1 + - + +
114E PRO 4.6 7.2 - - - +
115E ASN* 4.7 5.6 - - - +
117E LEU* 4.1 20.4 - - + +
119E GLN* 4.0 23.1 - - + +
312E GLY* 1.3 86.8 - - - +
314E LEU* 1.3 62.3 + - - +
315E GLY 4.3 1.1 - - - +
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Residues in contact with LEU 314 (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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23E PHE* 4.7 13.2 - - + -
37E TRP* 4.1 14.1 - - + -
78E SER* 3.3 1.4 - - - -
79E ALA* 2.9 38.6 + - - +
81E PHE* 3.5 9.3 - - + -
93E VAL* 4.9 3.8 - - + -
94E GLN 6.1 0.4 - - - +
95E PHE* 6.0 0.4 - - + -
110E VAL* 4.1 23.1 - - + -
111E LYS 3.3 8.7 - - - +
112E LEU* 3.9 10.5 - - + -
313E VAL* 1.3 74.1 - - - +
315E GLY* 1.3 66.8 + - - +
316E LEU* 4.7 0.9 - - + +
330E PHE* 4.0 37.0 - - + -
332E ILE* 3.8 25.6 - - + -
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Residues in contact with GLY 315 (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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77E LEU 3.6 7.2 - - - -
78E SER* 3.8 9.0 - - - -
110E VAL* 3.6 6.4 - - - +
111E LYS* 2.8 40.8 + - - +
113E PHE* 4.1 5.5 - - - -
122E MET* 4.0 11.4 - - - -
313E VAL 4.1 1.4 - - - -
314E LEU* 1.3 74.7 - - - +
316E LEU* 1.3 65.1 + - - -
317E ASP* 3.7 3.0 + - - -
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Residues in contact with LEU 316 (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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37E TRP* 4.1 13.5 - - + -
49E PHE* 3.9 31.3 - - + -
66E LEU* 3.8 28.9 - - + -
75E TYR 3.8 1.0 - - - -
76E ALA* 3.3 6.4 + - - -
77E LEU* 2.8 35.1 + - + +
109E TYR 4.2 9.6 - - - +
110E VAL* 3.8 28.5 - - + -
122E MET* 3.6 0.6 - - - +
314E LEU* 4.7 0.7 - - + -
315E GLY* 1.3 71.8 - - - +
317E ASP* 1.3 59.8 + - - +
318E LEU* 4.1 6.5 - - + -
327E PHE* 4.1 21.5 - - + -
330E PHE* 4.1 17.7 - - + -
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Residues in contact with ASP 317 (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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46E PHE* 5.4 1.6 - - - -
75E TYR 3.3 12.6 - - - +
76E ALA* 3.9 6.1 - - - +
109E TYR* 3.5 18.9 + - - -
111E LYS* 3.5 33.7 + - + +
113E PHE* 5.1 0.8 - - + -
122E MET* 4.0 18.4 - - + -
123E HIS* 3.2 27.4 + - - +
124E GLY* 3.2 26.6 + - - -
315E GLY 3.7 3.0 + - - -
316E LEU* 1.3 75.8 - - - +
318E LEU* 1.3 65.1 + - - +
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Residues in contact with LEU 318 (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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49E PHE* 5.2 0.4 - - + -
68E THR* 4.8 5.2 - - + -
73E ARG 4.0 0.3 - - - +
74E PHE* 3.3 8.9 - - - +
75E TYR* 2.7 53.4 + - + +
107E GLY* 3.8 22.0 - - - +
109E TYR* 3.6 44.0 - - + +
316E LEU* 4.5 7.6 - - + -
317E ASP* 1.3 82.6 + - - +
319E TRP* 1.3 62.5 + - - +
320E GLN* 4.0 20.4 - - + +
327E PHE* 3.9 23.6 - - + -
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Residues in contact with TRP 319 (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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72E ALA* 3.4 32.5 - - + -
73E ARG* 3.3 37.2 - - - -
74E PHE* 3.6 44.4 - + + -
105E CYS* 4.8 14.4 - - - -
106E GLY* 3.3 5.4 - - - -
107E GLY* 3.0 25.7 + - - +
109E TYR* 4.8 3.4 + - - +
318E LEU* 1.3 76.1 - - - +
320E GLN* 1.3 72.4 + - - +
321E VAL* 3.7 24.8 - - + +
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Residues in contact with GLN 320 (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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68E THR* 2.5 35.0 + - + +
70E GLN 4.7 0.2 - - - +
72E ALA* 3.0 19.9 + - - -
73E ARG 3.0 17.5 + - - -
75E TYR* 4.2 12.1 - - + -
103E ILE* 3.8 12.1 - - + +
105E CYS 3.9 3.6 - - - -
106E GLY* 4.0 5.8 - - - -
107E GLY 3.1 21.0 + - - +
318E LEU* 4.0 11.1 - - + +
319E TRP* 1.3 86.2 - - - +
321E VAL* 1.3 65.0 + - - +
322E LYS 4.3 2.7 - - - +
323E SER* 3.6 11.5 - - - -
325E THR* 2.9 29.9 + - - +
327E PHE* 5.0 0.6 - - - -
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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