Contacts of the strand formed by residues 125 - 134 (chain C) in PDB entry 4ICX
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 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C GLY* 3.5 2.1 - - - -
18C ARG* 3.0 68.0 + - + -
19C HIS* 5.0 2.6 + - - +
20C PHE* 4.2 1.5 - - - -
111C TRP* 3.8 23.7 - - + +
112C TYR 3.2 20.6 - - - +
113C GLN* 3.9 15.2 + - + +
114C LEU* 4.4 1.1 - - - +
123C LYS 3.9 10.1 - - - +
124C SER* 1.3 76.8 - - - +
126C ILE* 1.3 63.8 + - - +
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Residues in contact with ILE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C ILE* 3.7 29.4 - - + -
16C GLU 3.4 12.3 - - - +
20C PHE* 4.2 17.3 - - + -
30C VAL* 5.6 7.2 - - + -
52C PHE* 4.3 22.2 - - + -
77C LEU* 6.4 0.2 - - + -
79C CYS* 4.4 23.6 - - + -
95C ILE* 3.7 24.5 - - + -
111C TRP* 3.9 2.7 - - - -
112C TYR 3.0 25.7 + - - +
114C LEU* 4.6 5.6 - - + -
125C GLU* 1.3 76.2 - - - +
127C GLN* 1.3 67.9 + - - +
128C ILE* 3.4 16.4 + - + +
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Residues in contact with GLN 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C LEU* 3.2 45.1 + - + +
16C GLU* 2.8 19.5 + - - +
109C PRO* 3.9 36.9 + - + +
110C LYS 4.0 4.9 - - - +
111C TRP* 3.3 57.1 - - + +
126C ILE* 1.3 72.1 - - - +
128C ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C VAL* 3.9 21.8 - - + -
13C SER 3.5 12.8 - - - +
14C ILE* 4.5 7.4 - - + -
15C LEU* 4.2 0.4 - - - -
77C LEU* 3.5 26.7 - - + -
95C ILE* 3.9 19.7 - - + -
97C LEU* 3.9 17.3 - - + -
109C PRO* 3.5 3.3 - - - +
110C LYS* 3.2 32.9 + - - +
112C TYR* 3.9 22.7 + - + +
126C ILE* 3.4 25.3 + - + +
127C GLN* 1.3 79.2 - - - +
129C SER* 1.3 67.7 + - - +
130C ILE* 5.8 0.7 - - + -
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Residues in contact with SER 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C VAL 3.7 1.1 - - - +
12C VAL* 3.5 2.6 - - - -
13C SER* 2.7 45.0 + - - +
15C LEU* 4.2 9.6 - - - -
106C LYS* 6.1 0.9 - - - +
107C GLN 3.7 15.3 + - - -
108C ALA 5.6 0.7 - - - -
109C PRO* 3.9 22.9 - - - -
112C TYR* 6.2 0.2 - - - -
128C ILE* 1.3 78.4 - - - +
130C ILE* 1.3 64.8 + - - +
131C ALA* 5.0 3.8 + - - +
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Residues in contact with ILE 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 3.8 6.1 - - + -
11C VAL 3.5 7.9 - - - +
12C VAL* 3.9 12.1 - - + -
75C ILE* 3.7 30.3 - - + -
97C LEU* 5.0 13.9 - - + -
98C ASP 4.4 15.0 - - - +
99C LEU* 3.7 17.5 - - + -
101C THR* 4.4 19.8 - - + +
102C ALA* 4.0 21.8 + - + +
103C GLN 4.7 0.9 + - - -
107C GLN* 4.7 15.0 + - - +
112C TYR* 5.0 10.8 - - - +
128C ILE* 5.8 0.9 - - + -
129C SER* 1.3 78.4 + - - +
131C ALA* 1.3 68.7 + - - +
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Residues in contact with ALA 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 3.7 0.5 - - - -
11C VAL* 3.0 44.8 + - + +
102C ALA* 4.3 3.8 - - - -
103C GLN 3.9 12.3 - - - +
106C LYS* 4.5 20.9 - - + +
107C GLN 5.3 1.3 - - - +
129C SER* 5.3 3.4 - - - +
130C ILE* 1.3 77.7 - - - +
132C LEU* 1.3 73.5 + - - +
133C GLU* 5.5 2.0 - - + +
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Residues in contact with LEU 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C LEU* 3.8 27.1 - - + -
9C LEU 3.3 3.4 - - - +
10C ILE* 3.8 28.5 - - + +
11C VAL* 5.3 0.2 - - - -
65C LEU* 3.8 13.9 - - + -
69C ARG* 3.7 28.0 - - - +
99C LEU* 4.8 0.4 - - + -
102C ALA* 3.8 29.6 - - + +
103C GLN* 3.3 10.5 + - - +
104C GLU* 3.5 36.2 - - + +
131C ALA* 1.3 86.1 - - - +
133C GLU* 1.3 69.2 + - - +
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Residues in contact with GLU 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LYS* 4.4 18.2 - - - +
66A HIS* 3.0 45.3 + - + +
67A GLN* 4.8 8.2 + - - +
70A LEU* 3.9 3.9 - - + +
8C LEU* 3.7 1.9 - - - +
9C LEU* 3.0 42.2 + - + +
11C VAL* 3.9 15.3 - - + +
104C GLU* 5.4 4.5 - - - +
131C ALA* 5.5 2.4 - - + +
132C LEU* 1.3 80.0 - - - +
134C THR* 1.3 68.7 + - - +
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Residues in contact with THR 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLN* 2.8 27.6 + - - -
70A LEU* 4.1 7.9 - - - -
6C ASP* 6.1 2.9 - - - -
7C GLN 4.4 5.2 - - - +
8C LEU* 3.5 23.1 - - + -
62C ARG* 3.4 28.9 - - - +
104C GLU* 3.8 23.9 + - + +
133C GLU* 1.3 78.6 - - - +
135C ASP* 1.3 66.1 + - - +
136C THR* 4.1 7.3 + - - +
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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