Contacts of the strand formed by residues 24 - 31 (chain D) in PDB entry 3U53
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.2 11.7 - - + -
12D ARG 3.5 7.6 - - - +
13D ARG* 3.9 29.4 - - + +
22D ASN* 3.5 14.3 - - - +
23D ALA* 1.3 90.4 - - + +
25D GLU* 1.3 70.1 + - - +
26D PHE* 4.1 23.6 - - + -
118D GLY* 3.6 9.0 - - - -
119D LEU 4.3 3.3 + - - -
139D HIS* 3.9 16.2 - - + +
142D LEU* 3.7 33.7 - - + -
143D CYS* 4.7 9.9 - - - -
157D SO4 2.7 16.0 + - - +
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Residues in contact with GLU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 3.2 4.0 - - - +
12D ARG* 2.7 80.0 + - + +
14D CYS* 3.7 16.1 - - - -
22D ASN* 4.1 16.8 + - + -
24D ILE* 1.3 78.4 - - - +
26D PHE* 1.3 62.4 + - - +
101D TYR* 3.3 6.6 + - - -
116D TRP* 3.8 17.3 - - + +
117D LEU 3.1 17.0 - - - +
118D GLY 4.1 3.2 + - - +
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Residues in contact with PHE 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ILE* 3.5 32.3 - - + -
10D ILE 3.4 8.3 - - - +
11D PHE* 3.8 15.9 - + + -
24D ILE* 4.1 14.1 - - + -
25D GLU* 1.3 73.2 - - - +
27D LEU* 1.3 63.8 + - - +
28D LEU* 4.0 4.2 + - + -
95D LEU* 4.6 8.5 - - + -
115D ARG 3.4 1.0 - - - +
116D TRP* 3.2 7.6 - - - -
117D LEU* 2.6 41.5 + - - +
119D LEU* 3.9 33.9 - - + -
122D ALA* 4.5 14.1 - - + -
135D LEU* 4.1 28.5 - - + -
138D GLY* 5.3 0.4 - - - -
139D HIS* 4.2 23.1 - + + -
142D LEU* 4.9 1.1 - - + -
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ILE* 3.1 29.7 + - + +
26D PHE* 1.3 74.3 - - - +
28D LEU* 1.3 69.5 + - - +
29D LEU* 4.2 15.5 - - + -
40D PRO* 3.8 14.9 - - - +
41D PRO* 4.4 4.6 - - + +
63D ALA* 4.4 7.4 - - + -
65D ILE* 4.3 16.2 - - + -
105D ILE* 4.0 23.8 - - + -
114D TYR* 3.9 31.2 - - + -
115D ARG 3.4 13.5 - - - +
116D TRP* 3.6 28.2 - - + -
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Residues in contact with LEU 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D PHE* 5.1 3.8 - - + +
27D LEU* 1.3 85.0 - - - +
29D LEU* 1.3 62.5 + - - +
38D TRP* 3.2 24.7 - - + +
39D THR* 3.7 6.5 - - - +
40D PRO* 3.6 28.9 - - + -
114D TYR* 3.2 5.0 - - - +
115D ARG 2.9 34.6 + - - +
117D LEU* 4.0 21.1 - - + -
122D ALA* 3.6 31.2 - - + +
125D LEU* 4.1 11.2 - - + -
126D ALA* 4.6 3.1 - - + +
131D MET* 6.1 0.7 - - + -
135D LEU* 4.9 15.3 - - + -
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Residues in contact with LEU 29 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27D LEU* 4.2 20.0 - - + -
28D LEU* 1.3 77.7 - - - +
30D GLN* 1.3 62.1 + - - +
31D ALA 4.1 0.2 + - - -
37D HIS 3.3 1.2 - - - +
38D TRP* 3.1 8.3 - - - -
39D THR 2.8 35.8 + - - +
40D PRO 4.9 0.2 - - - -
41D PRO* 4.3 21.8 - - + -
62D GLU* 3.9 25.6 - - + +
63D ALA* 4.6 5.6 - - + +
105D ILE* 4.8 1.1 - - + -
107D LEU* 3.8 19.7 - - + -
111D HIS* 3.6 40.9 + - + +
113D ALA 3.5 4.9 - - - +
114D TYR* 3.8 13.0 - - + -
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Residues in contact with GLN 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D LEU* 1.3 70.8 - - - +
31D ALA* 1.3 60.6 + - - +
35D ILE* 3.6 23.4 + - - +
36D HIS* 5.1 1.0 - - - +
37D HIS 3.0 12.3 - - - +
38D TRP* 3.5 43.8 - - + +
111D HIS* 2.7 34.7 - - - +
112D GLN* 2.4 38.4 + - - +
113D ALA* 2.9 21.3 + - - +
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Residues in contact with ALA 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D GLN* 1.3 72.0 - - - +
32D SER* 1.3 63.6 + - - +
33D ASP* 3.7 16.8 - - + +
35D ILE* 3.4 19.8 - - - -
37D HIS* 2.7 32.9 + - + +
110D GLU 3.4 3.6 - - - +
111D HIS* 3.3 18.4 + - + +
112D GLN* 3.7 5.7 - - - +
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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