Contacts of the strand formed by residues 28 - 36 (chain D) in PDB entry 2IAN
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 VAL 28 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D ILE 3.5 25.1 - - - +
2D GLN 4.0 8.7 - - - +
3D VAL* 4.6 1.1 - - + -
24D PHE* 3.5 33.4 - - + -
25D SER 3.1 16.2 + - - +
26D ASP* 3.1 5.4 + - - +
27D SER* 1.3 86.5 - - - +
29D ASN* 1.3 74.7 + - - +
88D ALA* 3.6 18.6 - - + -
89D LEU 3.4 7.4 - - - +
90D ILE* 3.8 19.5 - - + +
91D GLN* 4.2 2.9 - - - +
97D VAL* 4.8 5.8 - - + -
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Residues in contact with ASN 29 (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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76B ASP 5.2 0.4 + - - -
77B THR* 3.2 30.7 + - + +
81B HIS* 4.8 7.9 + - - +
24D PHE* 3.8 21.1 - - - -
26D ASP 5.2 0.8 + - - -
28D VAL* 1.3 80.4 + - - +
30D ASN* 1.3 84.4 + - - +
31D LEU* 3.4 13.3 - - - +
49D PRO 4.4 1.7 - - - +
64D ALA* 4.1 12.1 + - - +
88D ALA* 3.4 1.6 - - - +
89D LEU* 2.6 39.6 + - - +
91D GLN* 3.8 24.3 - - - +
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Residues in contact with ASN 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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70B GLN* 4.0 15.3 - - - +
77B THR* 4.0 24.6 + - - +
29C LEU* 5.7 3.6 - - - +
29D ASN* 1.3 95.1 + - - +
31D LEU* 1.3 67.8 + - - +
32D GLN* 3.6 9.4 + - - +
47D TYR* 2.6 40.4 + - + +
49D PRO* 3.6 16.7 - - - +
87D ALA 4.4 1.4 - - - +
88D ALA* 4.7 1.2 - - - -
89D LEU* 4.3 23.2 + - + +
91D GLN* 5.1 5.5 + - - -
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Residues in contact with LEU 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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22D CYS* 3.8 17.7 - - - -
24D PHE* 3.4 60.1 - - + -
29D ASN* 3.9 5.4 - - - +
30D ASN* 1.3 90.8 - - - +
32D GLN* 1.3 62.9 + - - +
33D TRP* 5.5 0.2 - - - +
47D TYR* 3.6 0.7 - - - -
48D ILE* 3.0 30.1 + - + +
49D PRO* 4.0 4.0 - - - +
62D THR* 4.0 20.2 - - + +
69D SER* 3.6 23.1 - - - +
86D CYS* 4.5 5.6 - - + -
87D ALA 3.5 9.6 - - - +
88D ALA* 4.2 6.3 - - + -
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Residues in contact with GLN 32 (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 ASN 3.6 10.3 + - - +
31D LEU* 1.3 82.2 - - - +
33D TRP* 1.3 69.5 + - - +
34D PHE* 3.8 17.7 - - + -
44D ASN* 2.7 27.7 + - - -
46D PHE 3.2 8.1 - - - +
47D TYR* 4.1 6.7 - - + -
48D ILE* 4.6 1.3 - - - -
86D CYS* 3.4 7.1 - - - +
87D ALA* 3.0 33.6 + - + +
89D LEU* 5.0 3.6 - - - +
96D LEU* 3.8 23.2 - - + +
94E THR* 3.9 5.9 - - - +
97E GLY 3.1 22.6 + - - -
98E THR* 3.5 2.9 - - - -
99E GLY* 2.8 20.6 + - - +
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Residues in contact with TRP 33 (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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5D GLN* 3.8 19.5 - - - -
20D LEU* 4.0 30.1 - - + -
21D ARG 4.3 0.9 - - - -
22D CYS* 3.6 30.7 - - + -
31D LEU* 5.5 0.4 - - - +
32D GLN* 1.3 80.8 + - - +
34D PHE* 1.3 57.7 + - - +
44D ASN* 3.5 4.9 + - - -
45D LEU* 2.6 48.4 + - + +
46D PHE 3.0 12.0 + - - +
48D ILE* 3.8 19.1 - - + -
60D ALA* 4.3 10.9 - - + +
69D SER* 3.2 22.1 + - - -
70D LEU 4.1 10.8 - - - +
71D LEU* 3.7 48.6 - - + +
84D TYR* 4.6 3.8 - - + -
85D PHE 3.5 16.2 - - - -
86D CYS* 3.8 6.5 - - + +
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Residues in contact with PHE 34 (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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32D GLN* 3.8 38.8 - - + -
33D TRP* 1.3 77.8 - - - +
35D HIS* 1.3 58.8 + - - +
42D LEU* 4.0 17.0 - - + -
43D ILE 3.3 21.8 - - - +
44D ASN* 3.8 11.2 - - - -
45D LEU* 3.9 4.8 - - - +
84D TYR* 3.3 9.4 - - - +
85D PHE* 2.6 46.1 + - + +
87D ALA* 4.3 5.2 - - + -
96D LEU* 5.3 2.2 - - + -
98D PHE* 3.6 26.7 - + + -
99E GLY* 3.6 27.4 - - - -
101E PHE* 3.7 32.8 - + - -
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Residues in contact with HIS 35 (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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34D PHE* 1.3 74.1 - - - +
36D GLN* 1.3 81.0 + - - +
37D ASN* 3.7 14.9 - - + +
41D GLN 3.5 5.7 - - - +
42D LEU* 4.4 3.1 - - - -
43D ILE* 3.3 29.6 + - + +
45D LEU* 3.8 23.6 - - + +
79D THR 4.5 5.9 + - - -
80D ASP* 3.3 14.8 - - - -
81D SER 2.8 31.7 + - - -
82D GLY* 4.0 2.0 - - - -
83D VAL 3.4 3.9 + - - -
84D TYR* 3.3 25.2 - + + -
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Residues in contact with GLN 36 (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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34D PHE 4.0 0.6 - - - -
35D HIS* 1.3 95.5 + - - +
37D ASN* 1.3 73.6 + - - +
40D GLY* 3.5 25.8 + - - +
41D GLN 3.0 12.3 - - - +
42D LEU* 3.9 21.3 - - + +
83D VAL* 2.7 32.7 + - + +
85D PHE* 3.5 17.6 - - + -
37E GLN* 2.5 44.3 + - - -
43E LEU* 5.3 0.4 - - - +
90E PHE* 4.1 5.5 - - - -
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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