Contacts of the helix formed by residues 98 - 106 (chain A) in PDB entry 1LWU
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 GLU 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ASN* 2.9 31.5 + - + -
97A LEU* 1.3 78.7 - - - +
99A VAL* 1.3 77.9 + - - +
100A ARG 3.5 0.2 - - - -
101A TYR* 4.1 1.6 - - - -
102A SER* 3.0 41.0 + - - +
89L LEU* 3.2 28.0 - - + -
93L ARG* 4.3 12.8 + - - +
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASN* 2.9 48.6 + - + +
96A GLU* 4.6 4.7 - - - +
98A GLU* 1.3 86.4 + - - +
100A ARG* 1.3 71.2 + - + +
102A SER* 4.3 0.2 - - - -
103A GLU* 3.1 39.3 + - + +
106A ARG* 4.9 0.3 + - - -
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Residues in contact with ARG 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLU 3.8 20.2 + - - +
97A LEU* 3.9 9.2 - - + +
98A GLU 4.6 0.2 - - - +
99A VAL* 1.3 79.3 - - + +
101A TYR* 1.3 67.8 + - - +
103A GLU* 2.9 14.3 - - - +
104A VAL* 2.7 28.3 + - + +
100J ARG* 6.1 0.7 - - + -
103J GLU* 4.7 10.8 + - - +
104J VAL* 3.2 24.8 - - + +
107J GLU* 2.5 53.9 + - - +
111J ARG* 4.9 1.2 - - - +
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Residues in contact with TYR 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A LEU 4.1 7.4 - - - +
98A GLU* 3.7 7.5 + - - +
99A VAL 3.4 0.2 - - - -
100A ARG* 1.3 76.3 - - - +
102A SER* 1.3 76.7 + - - +
104A VAL* 2.7 29.4 + - + +
105A LEU* 2.9 47.1 + - + +
164B GLN* 4.8 10.7 + - - +
85C VAL* 4.5 16.4 - - + +
101J TYR* 4.7 14.4 - + - -
104J VAL* 3.6 24.5 - - + +
85L VAL* 4.0 44.5 - - + +
86L GLN* 3.7 26.3 + - - +
89L LEU* 4.9 13.9 - - + -
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Residues in contact with SER 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 3.0 34.8 + - - +
99A VAL 4.3 0.2 - - - -
101A TYR* 1.3 91.5 - - - +
103A GLU* 1.3 51.8 + - - +
105A LEU* 3.3 11.5 - - - +
106A ARG* 2.6 48.2 + - - +
86L GLN* 4.7 4.9 + - - -
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Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL* 3.1 31.9 + - + +
100A ARG* 2.9 28.9 + - - +
102A SER* 1.3 72.6 - - - +
104A VAL* 1.3 62.5 + - + +
105A LEU 3.0 5.4 - - - -
106A ARG* 3.0 26.4 - - + +
107A GLU* 3.0 25.8 + - - +
100J ARG* 5.0 9.5 + - - +
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Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ARG* 2.7 23.8 + - + +
101A TYR* 3.3 11.7 - - - +
103A GLU* 1.3 81.3 - - + +
105A LEU* 1.3 60.9 + - + +
107A GLU* 3.3 8.3 + - - +
108A LEU* 3.4 5.2 + - - +
89C LEU* 5.5 3.4 - - + -
97J LEU* 3.3 42.8 - - + +
100J ARG* 3.3 33.9 - - + +
101J TYR* 4.1 24.2 - - + -
104J VAL* 4.6 8.3 - - + -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A TYR* 2.9 49.4 + - + +
102A SER* 3.3 13.9 - - - +
104A VAL* 1.3 78.7 - - + +
106A ARG* 1.3 56.2 + - - +
107A GLU 2.9 8.2 + - - -
108A LEU* 3.2 22.3 + - + +
109A GLU* 3.7 5.7 + - - +
163B ALA* 4.1 27.6 - - - +
164B GLN* 4.4 5.8 - - + +
167B ILE* 3.5 27.7 - - + +
85C VAL* 4.6 13.9 - - + -
101J TYR* 6.4 0.4 - - + -
86L GLN* 5.5 2.0 - - - +
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A VAL 4.9 0.4 + - - -
102A SER* 2.6 53.2 + - - +
103A GLU* 3.0 25.1 - - + +
105A LEU* 1.3 75.0 - - - +
107A GLU* 1.3 57.2 + - - +
108A LEU 3.5 0.4 - - - -
109A GLU* 4.4 15.1 - - - +
110A ARG* 3.8 15.9 + - - +
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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