Contacts of the strand formed by residues 23 - 34 (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 ARG 23 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ARG* 5.1 0.7 + - - -
21C PRO* 3.0 16.9 + - + +
22C LYS* 1.3 74.3 - - - +
24C PRO* 1.3 67.5 - - + +
25C LYS 3.3 1.9 + - - -
26C HIS* 3.2 52.3 + - + +
46C HIS* 2.8 58.1 + - + +
81C ALA* 3.7 17.0 - - - +
90C GLU* 4.2 14.6 + - - -
92C ILE* 4.6 0.8 - - - +
118C LYS* 5.9 0.6 - - - +
119C TYR* 2.8 42.5 + - - -
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Residues in contact with PRO 24 (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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6B ASP* 5.4 5.5 - - - +
62B ARG* 3.2 21.5 + - - +
22C LYS 3.5 10.3 - - - +
23C ARG* 1.3 84.4 - - + +
25C LYS* 1.3 68.5 - - + +
26C HIS 3.5 0.2 - - - -
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Residues in contact with LYS 25 (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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6B ASP* 5.4 17.3 - - - +
62B ARG* 3.7 9.2 - - - +
134B THR* 5.8 7.1 - - - +
23C ARG 3.3 0.6 - - - -
24C PRO* 1.3 90.2 - - + +
26C HIS* 1.3 76.8 + - + +
83C ASP* 4.2 13.9 - - - +
84C PRO* 4.2 3.7 - - - +
85C VAL* 6.5 0.9 - - + -
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Residues in contact with HIS 26 (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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62B ARG* 3.3 12.4 + - - +
23C ARG* 3.2 59.3 + - + +
24C PRO* 3.5 1.0 - - - +
25C LYS* 1.3 97.1 + - + +
27C MSE 1.3 67.3 + - - +
46C HIS* 3.4 24.5 + - + +
81C ALA* 5.0 4.0 - - + -
82C LEU 3.4 18.8 - - - +
83C ASP* 4.1 23.5 + - + +
84C PRO* 4.5 1.8 - - - -
90C GLU* 5.7 1.1 + - - -
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Residues in contact with MSE 27 (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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61B ASP* 5.6 0.2 - - - +
62B ARG* 3.5 28.0 - - + +
63B LYS* 3.5 37.5 - - + -
66B HIS* 6.1 0.2 - - - -
26C HIS* 1.3 78.9 - - - +
28C LEU* 1.3 65.3 + - - +
43C PRO* 4.1 24.5 - - + +
44C VAL 3.3 14.6 - - - +
45C ASP* 3.4 25.8 - - - +
46C HIS* 4.1 4.5 - - - -
80C PHE 3.5 2.1 - - - +
81C ALA* 3.5 3.6 - - - -
82C LEU* 2.7 51.4 + - + +
84C PRO* 4.2 17.5 - - + -
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Residues in contact with LEU 28 (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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20C PHE* 3.8 21.1 - - + -
27C MSE 1.3 71.1 - - - +
29C VAL* 1.3 62.5 + - - +
42C ASP 4.2 1.2 - - - +
43C PRO* 3.4 4.2 - - - +
44C VAL* 2.8 47.0 + - + +
46C HIS* 3.6 37.9 - - + +
50C PRO* 3.6 35.7 - - + -
52C PHE* 4.0 15.6 - - + -
79C CYS* 3.9 17.0 - - - -
80C PHE 3.4 17.3 - - - +
81C ALA* 4.5 2.0 - - + +
92C ILE* 5.1 4.3 - - + -
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Residues in contact with VAL 29 (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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66B HIS* 4.9 5.2 - - - +
28C LEU* 1.3 78.6 - - - +
30C VAL* 1.3 67.1 + - - +
31C GLU* 4.5 13.9 - - + +
40C ALA* 4.5 5.2 - - + -
41C THR* 3.7 19.1 - - - +
43C PRO* 3.8 31.6 - - + -
52C PHE* 5.0 2.0 - - - -
78C GLN 3.8 0.5 - - - +
79C CYS* 3.8 1.5 - - - -
80C PHE* 2.7 50.5 + - + +
82C LEU* 4.0 20.9 - - + -
89C LYS* 5.7 5.6 - - + -
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Residues in contact with VAL 30 (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 16.2 - - + -
29C VAL* 1.3 73.3 - - - +
31C GLU* 1.3 63.0 + - - +
32C ALA 4.2 0.7 + - - -
40C ALA* 3.4 1.2 - - - -
41C THR* 2.9 56.3 + - + +
52C PHE* 4.0 18.6 - - + -
56C LEU* 4.8 1.6 - - - +
77C LEU* 3.8 37.5 - - + -
78C GLN 3.3 15.5 - - - +
79C CYS* 4.4 9.9 - - + -
126C ILE* 5.6 6.5 - - + -
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Residues in contact with GLU 31 (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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29C VAL* 4.2 7.4 - - + +
30C VAL* 1.3 74.5 - - - +
32C ALA* 1.3 57.4 + - - +
38C GLN* 3.6 27.7 + - + +
39C LEU 3.3 7.9 - - - +
40C ALA* 3.7 21.7 - - + +
76C LYS 3.5 1.9 - - - +
78C GLN* 2.7 41.9 + - + +
80C PHE* 3.3 27.4 - - + -
89C LYS* 2.9 28.8 + - - -
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Residues in contact with ALA 32 (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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30C VAL 4.1 1.0 + - - -
31C GLU* 1.3 73.9 - - - +
33C LYS* 1.3 61.2 + - - +
38C GLN* 3.4 4.4 - - - +
39C LEU* 2.9 31.9 + - - +
56C LEU* 3.6 17.4 - - + +
58C TRP* 3.6 18.3 - - + -
75C ILE* 4.5 4.0 - - + -
76C LYS 3.2 9.2 - - - +
77C LEU* 3.6 27.8 - - + -
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Residues in contact with LYS 33 (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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32C ALA* 1.3 75.9 - - - +
34C PHE* 1.3 60.6 + - - +
35C ASP 4.4 0.3 + - - -
36C GLY* 3.8 32.0 + - - +
37C GLU 3.5 11.4 - - - +
38C GLN* 4.3 26.2 + - + +
58C TRP* 4.6 0.7 - - - -
74C PRO 4.1 4.9 - - - +
75C ILE* 5.1 0.7 - - - -
76C LYS* 3.2 32.5 + - + +
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Residues in contact with PHE 34 (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 20.9 - - + -
33C LYS* 1.3 74.3 - - - +
35C ASP* 1.3 83.7 + - + +
36C GLY 3.2 1.6 - - - -
37C GLU* 3.0 25.9 + - - +
58C TRP* 3.8 33.0 + + + +
59C GLU 5.8 1.1 - - - -
60C ILE* 3.8 12.8 - - + -
68C HIS* 3.8 19.7 - + - -
73C THR* 3.9 22.7 - - + -
74C PRO 3.9 9.0 - - - -
75C ILE* 3.5 29.4 - - + -
99C LEU* 3.6 32.1 - - + -
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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