Contacts of the strand formed by residues 125 - 133 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B GLY* 3.3 3.6 - - - -
18B ARG* 2.8 77.8 + - + +
19B HIS* 4.3 5.5 - - - -
20B PHE* 3.5 1.2 - - - -
111B TRP* 4.0 16.2 - - + +
112B TYR 3.1 22.9 - - - +
113B GLN* 3.9 18.6 + - + +
114B LEU 4.3 1.3 - - - +
123B LYS* 3.8 12.8 - - - +
124B SER* 1.3 73.8 - - - +
126B ILE* 1.3 64.6 - - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 3.7 27.4 - - + -
16B GLU 3.4 11.2 - - - +
17B GLY* 4.5 0.4 - - - -
20B PHE* 3.9 19.1 - - + -
30B VAL* 4.2 19.3 - - + -
52B PHE* 4.2 16.6 - - + -
77B LEU* 6.0 0.7 - - + -
79B CYS* 4.5 5.4 - - + -
95B ILE* 3.9 15.9 - - + -
111B TRP* 3.6 3.8 - - - -
112B TYR* 2.9 28.3 + - - +
114B LEU* 3.9 21.8 - - + -
125B GLU* 1.3 80.7 - - - +
127B GLN* 1.3 65.0 + - - +
128B ILE* 3.5 17.4 + - + +
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B ILE* 4.0 0.2 - - - -
15B LEU* 3.0 45.8 + - + +
16B GLU* 2.7 49.9 + - - +
109B PRO* 3.8 24.6 - - + +
110B LYS 3.2 12.6 - - - +
111B TRP* 3.4 36.1 + - + +
126B ILE* 1.3 70.3 - - - +
128B ILE* 1.3 65.6 + - - +
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Residues in contact with ILE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B VAL* 3.9 17.0 - - + -
13B SER 3.3 10.1 - - - +
14B ILE* 4.5 6.5 - - + -
77B LEU* 3.7 26.0 - - + -
95B ILE* 4.1 13.5 - - + -
97B LEU* 3.9 22.4 - - + -
109B PRO* 3.4 4.0 - - - +
110B LYS* 2.8 32.9 + - - +
112B TYR* 3.9 27.8 - - + -
126B ILE* 3.8 20.6 - - + +
127B GLN* 1.3 80.1 - - - +
129B SER* 1.3 73.9 + - - +
130B ILE* 5.4 0.9 - - + -
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Residues in contact with SER 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B VAL 3.8 0.6 - - - +
12B VAL* 3.5 3.1 - - - -
13B SER* 2.8 49.3 + - - -
15B LEU* 5.3 3.0 - - - +
107B GLN 4.0 16.2 - - - -
108B ALA 4.2 1.8 - - - -
109B PRO* 3.7 24.0 - - - +
128B ILE* 1.3 79.3 - - - +
130B ILE* 1.3 63.5 + - - +
131B ALA* 6.5 0.2 - - - -
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Residues in contact with ILE 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.8 14.6 - - + -
11B VAL 3.4 9.4 - - - +
12B VAL* 3.8 16.6 - - + -
75B ILE* 3.8 30.3 - - + -
97B LEU* 4.6 15.0 - - + -
98B ASP 4.5 7.4 - - - +
99B LEU* 4.6 1.8 - - + -
101B THR* 3.5 33.0 - - - +
102B ALA* 3.8 24.0 - - + -
103B GLN* 4.5 1.0 + - - +
105B THR 5.3 0.7 - - - +
107B GLN* 5.3 9.6 + - - +
112B TYR* 5.3 6.1 - - - +
128B ILE* 5.8 0.2 - - + -
129B SER* 1.3 78.2 - - - +
131B ALA* 1.3 66.3 + - - +
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Residues in contact with ALA 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ILE* 3.5 7.1 - - - +
11B VAL* 2.9 38.3 + - + +
102B ALA* 4.2 4.3 - - - -
103B GLN 3.6 11.4 - - - +
105B THR 4.4 5.8 - - - +
106B LYS* 3.9 36.3 - - + +
107B GLN 5.4 0.2 - - - +
129B SER* 6.5 0.2 - - - -
130B ILE* 1.3 76.6 - - - +
132B LEU* 1.3 66.5 + - - +
133B GLU 4.2 0.2 - - - -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.5 9.6 - - + -
9B LEU 3.3 4.3 - - - +
10B ILE* 4.0 24.5 - - + -
65B LEU* 3.9 30.7 - - + -
69B ARG* 4.3 3.8 - - - +
99B LEU* 4.6 1.1 - - + -
102B ALA* 4.1 15.9 - - + +
103B GLN* 2.8 33.1 + - - +
104B GLU* 3.4 30.9 - - + +
106B LYS* 3.7 4.1 + - - -
131B ALA* 1.3 79.1 - - - +
133B GLU* 1.3 61.5 - - - +
134B THR* 5.9 1.1 - - + -
85C VAL* 3.6 35.2 - - + +
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Residues in contact with GLU 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.4 4.0 - - - +
9B LEU* 2.7 45.2 + - + +
11B VAL* 3.8 28.6 - - + +
55B GLU* 4.9 5.2 - - - +
106B LYS* 3.7 26.2 - - - +
131B ALA 4.2 0.4 - - - -
132B LEU* 1.3 74.6 - - - +
134B THR* 1.3 65.0 + - - +
135B ASP* 3.4 27.6 + - + +
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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