Contacts of the strand formed by residues 140 - 146 (chain L) in PDB entry 5A2Q
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 140 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3522 U 3.6 28.3 - - - -
3532 C 3.9 3.6 - - - -
71L ARG* 4.2 5.6 - - + -
73L LEU* 3.5 29.6 - - + -
109L MET* 3.6 26.0 - - + -
110L SER 4.6 2.2 + - - +
111L VAL* 3.3 24.0 - - + -
112L HIS 3.6 12.0 + - - -
128L VAL* 3.5 13.0 - - + -
129L GLY 3.1 23.1 - - - -
130L GLU* 3.4 31.6 - - + -
131L CYS* 4.2 1.8 - - - +
134L LEU* 3.6 16.8 - - - +
138L VAL* 3.5 3.6 - - - +
139L ARG* 1.3 92.6 - - + +
141L ASN* 1.3 65.9 + - - +
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Residues in contact with ASN 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59L LYS 3.2 22.2 + - - -
61L PRO* 3.2 25.0 - - + +
66L VAL* 4.0 15.6 - - - +
68L ILE* 4.0 19.7 - - + -
111L VAL* 3.4 7.2 - - - +
112L HIS* 3.5 16.6 + - - +
114L SER 5.1 0.9 + - - -
128L VAL* 3.3 1.2 - - - -
129L GLY 2.9 29.8 + - - +
131L CYS* 4.4 4.1 - - + +
134L LEU* 3.6 18.0 - - - +
140L PHE* 1.3 79.0 - - - +
142L VAL* 1.3 69.9 + - - +
143L LEU* 3.3 3.7 + - + +
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Residues in contact with VAL 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61L PRO* 4.1 9.5 - - - +
62L PHE* 4.7 0.2 - - - -
86L ILE* 4.1 12.8 - - + -
111L VAL* 4.2 11.9 - - + -
112L HIS 3.1 20.9 + - - +
113L LEU* 3.7 31.4 - - + -
114L SER 5.5 0.5 + - - -
117L PHE* 3.3 25.0 - - + -
126L VAL* 3.5 33.0 - - + -
127L THR 4.2 2.5 - - - -
128L VAL* 4.3 2.2 - - + +
141L ASN* 1.3 73.4 + - - +
143L LEU* 1.3 65.6 + - - +
144L LYS 4.1 3.4 - - - +
145L VAL* 4.0 8.1 - - + -
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Residues in contact with LEU 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L ILE* 4.8 7.9 - - + -
42L LEU* 5.8 0.4 - - + -
44L PHE* 3.6 49.0 - - + +
47L PRO* 5.5 0.3 - - - +
61L PRO* 4.2 15.7 - - + -
62L PHE* 3.7 15.5 - - + -
68L ILE* 3.7 44.2 - - + -
72L ILE* 5.3 2.7 - - + -
117L PHE* 3.3 15.1 - - - -
127L THR 3.0 11.8 + - - +
128L VAL 4.8 0.9 - - - -
129L GLY* 4.0 13.2 - - - +
141L ASN 3.3 11.6 + - - +
142L VAL* 1.3 80.4 - - - +
144L LYS* 1.3 65.3 + - - +
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Residues in contact with LYS 144 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44L PHE* 3.9 29.5 - - + -
117L PHE* 4.1 6.7 - - + -
126L VAL* 3.8 1.6 - - - +
127L THR* 3.0 51.9 + - - +
142L VAL* 3.7 1.6 - - - -
143L LEU* 1.3 82.0 - - - +
145L VAL* 1.3 68.5 + - - +
146L THR* 3.4 32.7 + - + -
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Residues in contact with VAL 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113L LEU* 4.8 1.3 - - + -
117L PHE* 4.3 19.7 - - + -
120L VAL* 3.6 36.3 - - + -
124L ASP* 3.9 16.6 - - - +
125L ILE 4.0 3.8 - - - +
126L VAL* 4.0 12.1 - - + -
142L VAL* 4.0 19.5 - - + -
144L LYS* 1.3 80.5 - - - +
146L THR* 1.3 68.4 + - - +
147L LYS* 4.2 9.2 + - + +
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Residues in contact with THR 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124L ASP* 3.7 2.1 - - - +
125L ILE* 2.6 65.1 + - + +
126L VAL* 5.1 0.4 - - - -
127L THR* 5.1 1.3 - - - +
144L LYS* 3.4 29.8 - - - +
145L VAL* 1.3 77.3 - - - +
147L LYS* 1.3 68.5 + - - +
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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