Contacts of the strand formed by residues 85 - 91 (chain X) in PDB entry 5LMQ
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 VAL 85 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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791A G 4.1 5.0 + - - -
84X GLU* 1.3 84.9 - - + +
86X LYS* 1.3 74.4 + - - +
87X SER* 4.0 5.6 + - - +
114X HIS* 5.5 0.2 - - - -
115X LYS* 3.1 29.2 - - + +
116X VAL 4.1 0.4 - - - -
117X LYS* 3.4 27.4 - - + +
164X LEU* 4.9 12.3 - - + -
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Residues in contact with LYS 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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788A U 4.2 4.2 + - - -
789A U 2.6 30.0 + - - -
791A G 3.6 15.3 - - - +
792A A 2.6 29.5 + - - +
84X GLU 4.0 0.8 + - - -
85X VAL* 1.3 75.0 - - - +
87X SER* 1.3 52.9 + - - +
88X ILE* 4.7 0.2 - - - -
109X PHE* 3.7 42.6 - - + -
112X GLU* 4.9 2.9 - - - -
114X HIS* 4.1 32.8 - - + -
115X LYS 2.8 9.9 + - - +
116X VAL* 3.2 9.4 - - + +
117X LYS 2.8 29.1 + - - -
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Residues in contact with SER 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A A 2.6 58.1 + - - +
791A G 3.2 19.9 + - - +
85X VAL* 4.5 5.3 + - - +
86X LYS* 1.3 74.7 - - - +
88X ILE* 1.3 61.0 + - - +
89X LYS* 6.0 0.7 - - - -
117X LYS* 3.4 21.1 - - - -
119X THR* 4.7 3.8 - - - -
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Residues in contact with ILE 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A A 3.4 2.5 - - - -
791A G 4.7 7.0 - - - +
87X SER* 1.3 82.8 - - - +
89X LYS* 1.3 64.1 + - - +
90X PHE* 3.7 28.3 + - + -
102X LYS* 3.8 27.8 - - + -
105X HIS* 5.0 4.5 - - + -
106X ILE* 3.7 25.4 - - + -
109X PHE* 3.6 37.5 - - + -
116X VAL* 3.9 11.2 - - + -
117X LYS 2.8 10.7 + - - +
118X VAL* 4.0 2.1 - - - -
119X THR* 2.8 32.2 + - - +
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Residues in contact with LYS 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A A 3.6 45.1 + - + +
1496A C 5.5 1.4 - - - +
1497A G 4.0 10.7 + - - +
87X SER* 6.0 0.7 - - - -
88X ILE* 1.3 77.4 - - - +
90X PHE* 1.3 67.4 + - - +
91X ARG* 4.3 9.9 + - - +
102X LYS* 3.8 13.6 + - - +
119X THR* 3.2 26.7 - - + +
121X MET* 3.5 46.2 - - + +
160X ASP* 5.5 4.2 + - - -
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Residues in contact with PHE 90 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1496A C 5.3 1.3 - - - -
88X ILE* 3.7 23.6 - - + -
89X LYS* 1.3 78.2 - - - +
91X ARG* 1.3 74.6 + - - +
94X ILE* 3.3 31.2 - - + -
99X TYR* 4.4 11.2 - + - -
102X LYS* 3.7 27.8 - - + +
103X LEU 5.0 0.2 - - - -
106X ILE* 3.8 10.8 - - + -
118X VAL* 3.7 27.4 - - + -
119X THR 2.8 15.2 + - - +
120X ILE* 4.2 14.6 - - + -
121X MET 3.8 13.7 + - - -
136X ILE* 3.5 29.2 - - + -
137X LEU* 4.8 5.6 - - + -
140X VAL* 4.1 13.9 - - + -
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Residues in contact with ARG 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1495A U 4.6 4.0 - - - +
1496A C 3.2 35.4 + - - +
1497A G 3.2 32.5 + - - -
89X LYS* 4.3 10.9 + - - +
90X PHE* 1.3 82.8 + - - +
92X VAL* 1.3 71.6 + - + +
93X LYS* 3.0 8.5 + - + +
94X ILE* 3.3 25.9 + - + +
120X ILE* 4.1 7.2 - - - -
121X MET* 3.4 36.4 - - - +
123X ARG* 4.2 32.1 - - - +
136X ILE* 4.1 4.6 - - - +
37Y U 6.0 2.6 - - - -
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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