Contacts of the strand formed by residues 91 - 99 (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 LEU 91 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E TYR* 5.0 0.2 - - + -
84E PHE* 3.6 34.1 - - + -
86E ASN* 4.0 19.7 - - + +
89E GLN 3.7 0.8 + - - -
90E THR* 1.3 75.0 - - - +
92E VAL* 1.3 66.5 + - - +
93E VAL* 4.3 9.4 - - + +
112E LEU* 4.3 9.6 - - + -
130E ILE* 3.9 28.0 - - + -
174E LEU* 3.7 1.3 - - + +
175E ILE* 3.5 2.1 - - - -
176E VAL* 2.8 49.2 + - + +
311E PHE* 3.9 18.8 - - + -
332E ILE* 3.8 17.5 - - + -
333E THR 3.8 3.8 - - - +
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Residues in contact with VAL 92 (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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90E THR* 4.0 17.0 - - + -
91E LEU* 1.3 78.2 - - - +
93E VAL* 1.3 66.5 + - - +
94E GLN* 4.2 2.2 - - + -
173E THR* 3.8 17.9 - - + -
174E LEU 3.3 9.4 - - - +
175E ILE* 4.2 10.3 - - + -
331E LEU 3.6 0.9 - - - +
332E ILE* 3.3 9.4 - - - +
333E THR* 2.8 48.0 + - + +
335E ASP 4.1 5.2 - - - +
336E GLU* 4.0 24.0 - - - +
339E ALA* 3.6 24.2 - - + -
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Residues in contact with VAL 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91E LEU* 4.3 13.7 - - + -
92E VAL* 1.3 76.3 - - - +
94E GLN* 1.3 63.9 + - - +
95E PHE* 4.7 3.4 - - + -
110E VAL* 4.1 25.8 - - + -
112E LEU* 3.3 34.5 - - + -
130E ILE* 5.8 1.6 - - + -
132E PHE* 4.0 11.9 - - + -
172E TYR 3.8 0.7 - - - +
173E THR* 3.4 1.9 - - - -
174E LEU* 2.8 55.2 + - + +
314E LEU* 4.9 2.9 - - + -
331E LEU 3.7 4.7 - - - +
332E ILE* 4.8 10.1 - - + +
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Residues in contact with GLN 94 (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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92E VAL* 4.7 4.7 - - + -
93E VAL* 1.3 77.5 - - - +
95E PHE* 1.3 70.3 + - - +
171E LEU* 3.6 21.0 - - + +
172E TYR 3.2 12.8 - - - +
173E THR* 2.8 31.2 + - + +
188E ASN* 4.5 2.3 - - - +
329E ASN 5.0 1.7 + - - +
330E PHE* 3.4 1.4 - - - +
331E LEU* 2.8 46.9 + - + +
339E ALA* 3.0 35.9 + - - +
342E PHE* 4.1 14.6 - - - -
343E GLY* 3.5 18.0 - - - +
346E THR* 5.2 0.2 + - - -
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Residues in contact with PHE 95 (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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93E VAL* 4.7 2.2 - - + -
94E GLN* 1.3 83.1 - - - +
96E THR* 1.3 65.3 + - - +
97E VAL* 3.3 31.9 - - + -
108E GLY 3.4 15.0 - - - -
110E VAL* 3.7 39.7 - - + -
132E PHE* 3.7 36.3 - + - -
133E GLY* 4.3 4.3 - - - -
134E PRO* 4.5 0.4 - - + -
171E LEU* 3.7 4.5 - - - +
172E TYR* 2.9 40.8 + - + +
314E LEU* 6.0 0.4 - - + -
327E PHE* 4.5 7.2 - + - -
328E ASP 3.8 4.5 - - - +
329E ASN 3.5 10.1 - - - -
330E PHE* 3.6 21.1 - + + -
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Residues in contact with THR 96 (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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95E PHE* 1.3 76.4 - - - +
97E VAL* 1.3 65.4 + - - +
169E THR* 3.6 27.3 - - + +
170E HIS 3.3 5.6 - - - +
171E LEU* 3.8 23.6 - - + -
326E ILE 4.4 1.0 + - - -
327E PHE* 3.4 6.1 - - - -
328E ASP* 2.9 56.3 + - - +
329E ASN* 3.5 18.3 + - + +
347E TRP* 4.0 15.7 - - + +
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Residues in contact with VAL 97 (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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95E PHE* 3.3 34.3 - - + -
96E THR* 1.3 73.2 - - - +
98E LYS* 1.3 61.4 + - - +
99E HIS* 3.8 28.3 - - + +
108E GLY 3.6 11.2 - - - +
134E PRO* 4.3 4.9 - - + -
168E PHE 3.6 2.1 - - - +
169E THR* 3.6 1.5 - - - -
170E HIS* 2.8 40.3 + - - +
172E TYR* 4.1 20.4 - - + -
325E THR* 3.9 17.5 - - + -
326E ILE 3.6 3.1 - - - -
327E PHE* 4.0 8.3 - - + -
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Residues in contact with LYS 98 (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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53E SER 3.5 9.9 + - - -
56E PHE* 2.7 45.4 + - - -
57E TYR* 4.4 3.2 - - - +
63E ASP* 5.6 4.4 + - - +
97E VAL* 1.3 75.1 - - - +
99E HIS* 1.3 60.0 + - - +
100E GLU* 3.1 34.2 + - + +
167E GLU 3.5 14.8 - - - +
168E PHE 3.7 5.8 - - - +
169E THR* 3.3 26.0 - - + +
324E GLY 4.0 0.5 - - - +
325E THR* 3.3 2.5 - - - -
326E ILE* 2.9 50.4 + - + +
354E GLU* 3.5 13.5 + - - +
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Residues in contact with HIS 99 (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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97E VAL* 3.8 18.7 + - + +
98E LYS* 1.3 69.6 - - - +
100E GLU* 1.3 58.7 + - - +
101E GLN* 3.0 16.0 + - - +
102E ASN* 3.1 9.5 + - - -
103E ILE* 3.7 40.1 - - + +
106E GLY 4.8 1.3 - - - -
107E GLY 4.3 13.2 - - - -
108E GLY* 4.4 3.5 + - - -
134E PRO* 4.7 10.9 - - + +
136E ILE* 4.0 20.4 - - + +
164E LYS 4.6 7.0 - - - -
165E ASP* 5.3 1.8 - - - +
166E ASP 3.6 13.4 + - - +
167E GLU* 3.4 16.6 - - - -
168E PHE 4.3 4.6 + - - -
325E THR* 2.7 37.6 + - + +
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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