Contacts of the strand formed by residues 123 - 131 (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 GLU 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ASN* 2.8 29.1 + - - +
17A PHE* 4.7 0.2 - - - -
116A THR* 3.8 17.1 - - + +
117A TYR 3.2 10.8 - - - +
118A THR* 4.3 11.2 - - + -
121A GLY 4.3 0.6 + - - -
122A VAL* 1.3 79.1 - - - +
124A ALA* 1.3 65.3 + - - +
125A LYS* 2.6 31.9 + - - -
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Residues in contact with ALA 124 (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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12A GLU 3.3 13.0 - - - +
13A ASN* 3.9 3.1 - - - +
14A TYR* 4.2 9.6 - - + -
17A PHE* 3.5 34.1 - - + -
116A THR* 3.4 4.0 - - - +
117A TYR* 2.9 42.2 + - + +
123A GLU* 1.3 76.4 - - - +
125A LYS* 1.3 65.4 + - - +
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Residues in contact with LYS 125 (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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11A ASN* 3.3 6.0 - - - +
12A GLU* 2.8 64.2 + - + +
14A TYR* 4.7 1.6 - - - +
114A ILE* 4.0 15.0 - - + -
115A GLN 3.3 8.3 - - - +
116A THR* 3.7 19.2 + - + +
117A TYR* 5.5 0.2 - - - -
123A GLU* 2.6 33.6 + - - +
124A ALA* 1.3 80.4 - - - +
126A ARG* 1.3 66.3 + - - +
127A ILE* 4.2 15.7 - - + -
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Residues in contact with ARG 126 (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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8A VAL* 3.9 20.4 - - + +
10A ARG 3.8 4.3 - - - -
11A ASN* 2.7 31.7 + - - +
14A TYR* 3.7 37.9 + - + -
31A GLY 3.8 7.5 + - - -
32A ALA 4.4 4.2 + - - -
34A ASP* 2.9 41.4 + - - +
36A LEU* 3.8 18.1 - - - +
115A GLN* 2.9 34.9 + - + +
117A TYR* 4.1 23.5 + - + +
125A LYS* 1.3 77.9 - - - +
127A ILE* 1.3 60.6 + - - +
128A PHE* 3.5 22.5 - - + -
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Residues in contact with ILE 127 (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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8A VAL* 3.8 1.5 - - - +
9A ASP* 2.8 25.5 + - - +
10A ARG* 2.9 72.0 + - + +
12A GLU* 4.1 23.3 - - + +
112A GLU* 3.9 18.8 - - + +
113A LEU 3.5 7.0 - - - +
114A ILE* 4.2 24.5 - - + -
125A LYS* 4.6 13.2 - - + -
126A ARG* 1.3 78.4 - - - +
128A PHE* 1.3 62.4 + - - +
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Residues in contact with PHE 128 (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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6A TRP* 3.9 29.8 - - + -
7A LYS 3.3 7.9 - - - +
8A VAL* 3.5 28.0 - - + -
9A ASP* 4.7 0.2 - - - -
36A LEU* 3.9 27.4 - - + -
38A LEU* 3.8 19.7 - - + -
112A GLU* 3.4 10.2 - - - +
113A LEU* 2.9 49.9 + - + +
115A GLN* 3.8 31.6 - - + -
126A ARG* 3.5 28.0 - - + -
127A ILE* 1.3 76.8 - - - +
129A LYS* 1.3 63.8 + - - +
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Residues in contact with LYS 129 (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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6A TRP* 3.5 3.3 - - - -
7A LYS* 2.9 36.7 + - + +
9A ASP* 3.4 35.5 + - + +
10A ARG* 4.2 1.2 - - - +
111A ASN* 4.6 7.8 - - - +
112A GLU* 3.1 29.5 + - + +
128A PHE* 1.3 76.7 - - - +
130A LYS* 1.3 67.8 + - - +
131A GLU* 4.7 0.2 - - - -
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Residues in contact with LYS 130 (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 4.5 9.5 + - - +
3A ASP 3.6 24.8 + - - -
4A GLY* 4.8 2.2 - - - -
5A THR 3.7 16.4 - - - +
6A TRP* 3.7 38.7 - - + -
111A ASN* 3.8 20.2 + - + +
129A LYS* 1.3 78.6 - - - +
131A GLU* 1.3 69.2 + - - +
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Residues in contact with GLU 131 (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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5A THR* 3.1 39.9 + - + +
6A TRP* 4.8 0.2 - - - +
7A LYS* 4.3 19.2 - - - +
37A LYS* 4.3 18.8 + - - +
129A LYS 3.6 1.8 + - - -
130A LYS* 1.3 82.9 - - - +
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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