Contacts of the strand formed by residues 100 - 105 (chain A) in PDB entry 1LC7
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 ARG 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A ARG* 1.3 123.5 - - - +
101A ALA* 1.3 61.1 + - - +
120A CYS* 3.7 0.9 - - - -
121A GLU* 3.3 29.8 + - + +
123A ARG* 3.5 24.7 - - - +
146A ASP* 2.7 43.7 + - - +
147A LEU* 4.1 10.1 - - + -
148A ASP* 2.9 36.6 + - - +
149A CYS 3.4 0.5 + - - -
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Residues in contact with ALA 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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98A PRO* 4.1 4.3 - - + -
100A ARG* 1.3 75.2 - - - +
102A MET* 1.3 60.9 + - - +
115A LEU* 4.1 19.3 - - + -
120A CYS* 3.4 18.1 - - - -
121A GLU 3.0 6.9 + - - -
122A ILE* 3.5 5.2 - - - +
123A ARG* 2.8 27.4 + - - +
147A LEU* 3.9 5.4 - - - +
149A CYS* 3.3 24.9 - - + +
151A PHE* 4.2 2.5 - - + -
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Residues in contact with MET 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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101A ALA* 1.3 75.2 - - - +
103A ILE* 1.3 77.7 + - - +
123A ARG* 3.2 25.4 - - + +
124A ARG 5.3 0.9 - - - -
125A TRP* 3.9 24.2 - - + +
139A ILE* 4.2 7.2 - - - -
142A ALA* 3.8 30.3 - - + +
143A LEU* 3.9 14.4 - - - -
147A LEU* 3.9 16.4 - - + +
149A CYS 2.9 9.8 + - - +
150A LEU* 3.3 24.3 - - + +
151A PHE* 2.9 28.6 + - - -
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Residues in contact with ILE 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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102A MET* 1.3 81.7 - - - +
104A VAL* 1.3 60.6 + - - +
105A THR* 4.3 11.4 - - + -
111A TYR* 4.2 21.1 - - + -
112A GLY* 4.6 16.8 - - - +
115A LEU* 3.7 28.3 - - + -
122A ILE* 4.1 12.8 - - + -
123A ARG 3.1 4.0 + - - +
124A ARG* 3.5 33.4 - - + +
125A TRP* 2.8 30.7 + - - +
151A PHE* 3.9 13.7 - - + +
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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
----------------------------------------------------------
103A ILE* 1.3 80.6 - - - +
105A THR* 1.3 65.6 + - - +
106A PRO 3.5 11.3 - - - +
107A GLY* 3.8 7.8 + - - -
111A TYR* 5.7 3.5 - - - -
125A TRP* 3.2 11.9 - - + +
127A LEU* 3.5 40.6 - - + -
135A LEU* 4.4 5.2 - - + -
139A ILE* 4.0 20.2 - - + -
150A LEU* 4.8 1.8 - - + -
151A PHE 3.9 6.8 + - - +
152A LEU* 3.6 32.1 - - + -
153A CYS 6.1 0.7 - - - +
156A ASN* 5.0 5.4 + - - +
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Residues in contact with THR 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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103A ILE* 4.3 10.8 - - + -
104A VAL* 1.3 77.3 - - - +
106A PRO* 1.3 66.3 - - + +
107A GLY 5.0 1.3 - - - +
124A ARG* 3.9 34.5 - - + +
125A TRP 3.0 10.4 + - - -
126A SER* 3.8 15.6 + - - -
127A LEU* 2.8 33.3 + - - +
329A PRO* 3.7 27.2 + - + +
330A GLY* 5.4 1.8 - - - -
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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