Contacts of the strand formed by residues 100 - 108 (chain A) in PDB entry 1ICM
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 LYS 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LYS* 3.4 3.4 - - - -
95A ARG* 3.0 27.4 + - - +
98A ASN* 3.0 40.0 - - - +
99A GLY* 1.3 79.8 - - - +
101A GLU* 1.3 61.7 + - - +
102A LEU 3.9 0.3 + - - -
119A TYR* 3.9 21.5 - - + +
120A GLU* 3.4 36.9 + - + +
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Residues in contact with GLU 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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92A LYS* 6.3 0.4 - - + -
93A PHE 3.5 11.0 - - - +
94A LYS* 4.5 14.0 + - - +
99A GLY 3.8 0.8 + - - -
100A LYS* 1.3 74.4 - - - +
102A LEU* 1.3 63.6 + - - +
103A ILE* 3.8 32.3 - - + +
118A THR 4.1 3.5 - - - +
119A TYR* 3.5 19.6 - - - -
120A GLU* 4.6 4.8 + - - +
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Residues in contact with LEU 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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17A PHE* 4.4 10.8 - - + -
21A MET* 4.3 29.2 - - + -
72A LEU* 6.0 0.2 - - + -
78A LEU* 4.5 20.2 - - + -
93A PHE* 2.9 51.4 + - + +
94A LYS* 5.2 0.4 - - - +
95A ARG* 5.5 2.2 - - + -
100A LYS 3.9 2.2 + - - +
101A GLU* 1.3 76.5 - - - +
103A ILE* 1.3 79.0 + - - +
104A ALA* 4.3 7.0 - - + +
117A TYR* 4.8 6.3 - - + -
118A THR 3.5 10.5 - - - +
119A TYR* 4.4 10.1 - - + -
133A MYR 4.4 25.8 - - + -
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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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90A VAL* 5.1 7.9 - - + -
91A GLY 3.3 11.2 - - - +
92A LYS* 4.2 20.2 - - + -
101A GLU* 3.8 35.7 - - + +
102A LEU* 1.3 82.3 - - - +
104A ALA* 1.3 73.0 + - - +
105A VAL* 4.4 11.4 - - + -
116A THR 3.8 0.2 - - - +
117A TYR* 3.3 4.9 - - - -
118A THR* 3.0 45.8 + - + +
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Residues in contact with ALA 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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82A TRP* 3.6 21.7 - - + -
91A GLY 2.6 41.2 + - - +
93A PHE* 4.6 7.9 - - + -
102A LEU* 4.2 6.9 + - + -
103A ILE* 1.3 75.5 - - - +
105A VAL* 1.3 67.4 - - - +
115A GLN* 6.5 0.2 - - + -
116A THR 3.2 9.0 - - - +
117A TYR* 3.9 20.0 - - + -
133A MYR 4.9 4.0 - - + -
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Residues in contact with VAL 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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82A TRP* 4.6 0.4 - - - -
88A LYS* 4.3 24.2 - - + +
89A LEU 3.4 11.0 - - - +
90A VAL* 4.8 11.4 - - + -
103A ILE* 4.4 13.0 - - + -
104A ALA* 1.3 82.1 - - - +
106A ARG* 1.3 74.8 + - - +
107A GLU* 4.4 13.7 - - - +
114A ILE 3.5 1.0 - - - +
115A GLN* 3.2 6.4 - - - +
116A THR* 2.9 45.7 + - + +
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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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2A PHE* 3.9 10.3 - - + -
38A LEU* 4.2 14.6 - - - +
40A ILE* 5.1 9.1 - - - +
49A VAL* 4.3 11.2 - - - +
62A PHE* 4.2 12.1 - - - -
82A TRP* 3.4 27.6 - - + +
88A LYS* 3.6 2.9 - - - +
89A LEU* 3.0 51.2 + - + +
105A VAL* 1.3 73.4 - - - +
107A GLU* 1.3 64.4 + - - +
113A LEU* 4.3 17.1 - - + +
114A ILE 3.4 3.8 - - - -
115A GLN* 2.4 48.2 + - + +
133A MYR 2.8 47.0 + - - +
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Residues in contact with GLU 107 (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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2A PHE* 4.3 4.3 - - - -
87A ASN 5.2 1.1 - - - +
88A LYS* 3.8 36.3 + - + +
105A VAL* 4.4 10.4 - - + +
106A ARG* 1.3 76.1 - - - +
108A ILE* 1.3 65.0 + - - +
109A SER* 5.5 0.8 - - - -
113A LEU* 3.6 6.4 - - - +
114A ILE* 2.8 63.9 + - + +
116A THR* 4.6 6.2 + - - -
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Residues in contact with ILE 108 (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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1A ALA* 3.7 23.6 - - - +
2A PHE* 3.7 34.7 - - + -
6A TRP* 4.1 20.2 - - + -
87A ASN 5.5 2.3 + - - +
107A GLU* 1.3 78.0 - - - +
109A SER* 1.3 62.9 + - - +
110A GLY 3.3 23.5 + - - +
111A ASN* 5.0 1.3 - - - -
112A GLU 3.3 9.4 - - - +
113A LEU* 4.3 5.8 - - + -
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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