Contacts of the strand formed by residues 24 - 31 (chain A) in PDB entry 4ICK
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 ILE 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PHE* 3.9 25.1 - - + -
12A ARG 3.5 3.6 - - - -
13A ARG* 4.3 13.7 - - + +
22A ASN* 3.5 16.8 - - - +
23A ALA* 1.3 84.6 - - + +
25A GLU* 1.3 63.4 + - - +
26A PHE* 3.9 29.2 - - + -
118A GLY* 3.8 6.8 - - - -
119A LEU 4.5 2.9 + - - -
139A HIS* 3.5 27.1 - - + +
142A LEU* 4.0 22.4 - - + -
143A CYS* 4.6 5.6 - - - -
146A GLU* 4.0 18.4 - - - +
201A GOL 3.3 11.4 + - - +
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Residues in contact with GLU 25 (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 PHE* 3.0 6.3 - - - +
12A ARG* 2.9 77.0 + - + +
14A CYS* 3.4 21.0 - - - +
20A ASP* 5.8 0.3 - - - +
22A ASN* 4.4 14.5 + - + +
24A ILE* 1.3 77.1 - - - +
26A PHE* 1.3 62.6 + - - +
101A TYR* 4.5 2.4 + - - -
116A TRP* 3.7 15.4 - - + +
117A LEU* 3.3 21.3 - - - +
118A GLY 4.0 3.0 + - - +
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Residues in contact with PHE 26 (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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9A ILE* 3.6 32.1 - - + -
10A ILE 3.4 7.4 - - - +
11A PHE* 4.1 13.2 - - + -
24A ILE* 3.9 20.2 - - + -
25A GLU* 1.3 73.7 - - - +
27A LEU* 1.3 63.2 - - - +
28A LEU* 3.7 4.2 + - + +
95A LEU* 4.7 7.4 - - + -
115A ARG 3.4 2.6 - - - +
116A TRP* 3.3 5.9 - - - -
117A LEU* 2.7 40.6 + - - +
119A LEU* 3.9 38.4 - - + -
122A ALA* 4.3 13.7 - - + -
135A LEU* 3.9 30.5 - - + -
138A GLY* 5.2 0.4 - - - -
139A HIS* 3.9 17.3 - + + -
142A LEU* 4.9 2.0 - - + -
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Residues in contact with LEU 27 (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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10A ILE* 2.9 29.0 + - + +
26A PHE* 1.3 71.3 - - - +
28A LEU* 1.3 69.2 + - - +
29A LEU* 4.0 16.4 - - + -
40A PRO* 3.7 18.2 - - - +
41A PRO* 4.3 6.1 - - + +
63A ALA* 4.2 6.5 - - + -
65A ILE* 3.9 28.5 - - + -
105A ILE* 3.9 10.8 - - + -
114A TYR* 3.7 38.6 - - + -
115A ARG 3.4 7.2 - - - +
116A TRP* 3.6 28.7 - - + +
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Residues in contact with LEU 28 (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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26A PHE* 4.7 5.4 - - + +
27A LEU* 1.3 79.9 - - - +
29A LEU* 1.3 64.6 + - - +
38A TRP* 3.8 20.5 - - + +
39A THR* 3.6 25.8 - - - +
40A PRO* 3.6 14.6 - - + -
114A TYR* 3.2 5.5 - - - +
115A ARG* 2.8 35.3 + - + +
117A LEU* 5.0 3.6 - - + -
122A ALA* 3.5 39.9 - - + +
125A LEU* 4.2 14.6 - - + -
126A ALA* 4.1 12.6 - - + +
135A LEU* 4.7 14.6 - - + -
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Residues in contact with LEU 29 (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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27A LEU* 4.0 20.9 - - + -
28A LEU* 1.3 75.5 - - - +
30A GLN* 1.3 60.3 + - - +
31A ALA 3.8 0.7 + - - -
37A HIS 3.5 1.7 - - - +
38A TRP* 3.3 4.9 - - - -
39A THR* 2.8 37.4 + - - +
40A PRO 5.2 0.4 - - - +
41A PRO* 4.2 21.5 - - + -
62A GLU* 3.7 40.2 - - + +
63A ALA* 4.4 3.4 - - + -
105A ILE* 4.7 1.1 - - + -
107A LEU* 3.9 11.7 - - + -
111A HIS* 3.6 28.2 - - + +
113A ALA 3.5 4.7 - - - +
114A TYR* 3.8 22.0 - - + -
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Residues in contact with GLN 30 (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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29A LEU* 1.3 71.8 - - - +
31A ALA* 1.3 64.8 + - - +
36A HIS* 3.7 31.6 + - + +
37A HIS 3.3 3.4 - - - -
38A TRP* 3.4 50.4 - - + +
111A HIS* 3.2 5.5 - - - -
112A GLN* 2.8 56.6 + - - +
113A ALA* 2.9 23.9 + - - +
115A ARG* 5.6 0.5 + - - -
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Residues in contact with ALA 31 (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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30A GLN* 1.3 76.5 - - - +
32A SER* 1.3 58.5 + - - +
33A ASP* 3.4 17.5 - - - +
36A HIS* 3.1 27.2 + - - +
37A HIS* 2.8 31.9 + - + +
110A GLU 3.6 9.2 - - - +
111A HIS* 3.6 11.1 - - + +
112A GLN* 3.8 2.6 - - - +
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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