Contacts of the strand formed by residues 27 - 38 (chain A) in PDB entry 4IYT
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 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A THR 4.2 0.3 - - - +
21A SER* 3.2 4.0 - - - -
22A SER 2.8 34.6 + - - +
25A TRP* 3.7 15.0 - - + +
26A GLY* 1.3 82.9 - - - +
28A THR* 1.4 69.5 + - - +
29A GLN* 4.2 0.4 - - + -
53A PHE* 3.4 5.8 - - - +
54A ILE* 4.1 15.9 - - + -
230A TYR* 3.5 51.6 - - + +
231A GLY* 5.0 0.9 - - - -
232A ARG* 4.3 1.8 - - - +
265A TYR* 3.7 32.8 - - + +
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Residues in contact with THR 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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19A ASP* 3.8 16.2 - - - +
20A THR 3.6 3.4 - - - +
21A SER* 2.6 27.5 + - - +
27A VAL* 1.4 74.8 - - - +
29A GLN* 1.4 61.9 - - - +
30A ASN* 3.6 22.9 - - - +
52A GLY* 3.2 5.6 - - - -
53A PHE* 2.8 44.5 + - - +
230A TYR* 3.4 8.1 - - - -
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Residues in contact with GLN 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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18A GLU 3.5 2.1 - - - +
19A ASP* 3.4 4.3 - - - -
20A THR* 2.8 39.5 + - + +
28A THR* 1.4 70.9 - - - +
30A ASN* 1.3 62.1 + - - +
31A ILE* 3.7 7.3 - - + +
228A ILE* 2.9 39.7 + - - +
230A TYR* 3.7 29.3 - - + +
265A TYR* 3.2 29.9 + - + -
267A VAL* 3.7 14.5 - - - +
269A TYR* 2.7 43.2 + - - +
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Residues in contact with ASN 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU 3.6 3.1 - - - -
19A ASP* 2.3 37.0 + - - +
28A THR* 3.6 10.1 - - - +
29A GLN* 1.3 69.5 - - - +
31A ILE* 1.3 59.6 + - - +
32A GLN* 5.4 2.7 + - - +
49A LYS 3.7 2.3 - - - +
51A GLN* 2.9 47.0 + - + +
52A GLY* 3.4 17.7 + - - +
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Residues in contact with ILE 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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17A THR* 3.2 7.0 - - - -
18A GLU* 2.8 38.2 + - + +
29A GLN* 3.8 15.9 - - + +
30A ASN* 1.3 76.5 - - - +
32A GLN* 1.3 69.3 + - - +
33A PHE* 3.6 32.9 - - + -
48A LEU* 4.5 4.7 - - + -
49A LYS 3.5 7.6 - - - +
50A MET* 4.0 10.1 - - + -
228A ILE* 3.9 24.7 - - + -
230A TYR* 3.4 26.5 - - + +
269A TYR* 3.5 27.6 - - + +
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Residues in contact with GLN 32 (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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16A ARG 3.6 4.5 - - - +
17A THR* 4.0 17.5 - - + -
30A ASN 5.4 2.6 + - - +
31A ILE* 1.3 77.3 - - - +
33A PHE* 1.3 60.6 + - - +
34A ASP* 3.9 4.9 - - - +
47A ILE 3.5 1.1 - - - +
48A LEU* 3.3 7.6 - - - -
49A LYS* 2.9 54.3 + - + +
51A GLN* 3.8 24.9 - - - +
133A LYS* 2.8 40.9 + - - +
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Residues in contact with PHE 33 (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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14A VAL 3.6 4.5 - - - +
16A ARG* 2.7 38.5 + - - +
18A GLU* 3.8 22.4 - - + -
31A ILE* 3.6 31.6 - - + -
32A GLN* 1.3 73.2 - - - +
34A ASP* 1.3 61.3 + - - +
35A PHE* 3.8 3.5 + - + -
46A LEU* 3.7 12.3 - - + -
47A ILE 3.7 2.9 - - - -
48A LEU* 3.6 31.9 - - + -
226A PHE* 5.5 1.6 - + + -
269A TYR* 3.8 33.0 - + + -
271A VAL* 4.2 21.1 - - + -
278A ILE* 3.1 36.3 - - + -
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Residues in contact with ASP 34 (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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13A VAL* 3.8 14.8 - - + -
14A VAL 3.6 3.6 - - - -
15A LYS* 3.7 15.7 - - - +
16A ARG 4.7 0.3 + - - +
32A GLN* 4.5 4.2 - - - +
33A PHE* 1.3 78.2 + - - +
35A PHE* 1.3 64.7 + - - +
36A VAL* 3.4 6.1 + - - +
46A LEU* 3.5 2.9 - - - +
47A ILE* 2.8 46.4 + - + +
131A TYR* 2.5 30.8 + - + +
133A LYS* 2.6 30.4 + - - +
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Residues in contact with PHE 35 (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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13A VAL* 3.3 6.3 - - - -
14A VAL* 2.8 46.3 + - + +
16A ARG* 4.2 5.6 - - + -
33A PHE* 4.0 9.2 - - + -
34A ASP* 1.3 69.8 - - - +
36A VAL* 1.3 61.1 + - - +
37A LYS* 3.5 4.1 + - + -
45A ALA 3.6 4.5 - - - +
46A LEU* 4.3 10.1 - - + -
271A VAL* 3.9 26.5 - - + -
272A ASN 4.0 12.6 - - - -
273A TRP* 4.1 31.4 - + - -
276A HIS* 3.4 61.9 - + + +
277A GLU 4.6 0.2 - - - -
278A ILE* 4.0 20.9 - - + -
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Residues in contact with VAL 36 (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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7A ILE* 4.6 8.5 - - + -
12A GLU 3.9 2.9 - - - -
13A VAL* 4.6 11.7 - - + +
34A ASP 3.9 6.5 - - - +
35A PHE* 1.3 70.6 - - - +
37A LYS* 1.3 59.4 + - - +
38A ASP* 3.8 8.0 + - + +
41A TYR* 5.2 2.8 - - + -
43A LYS 4.8 4.2 - - - +
44A ASP* 5.1 1.2 - - - -
45A ALA* 2.9 39.4 + - + +
47A ILE* 3.8 32.1 - - + -
111A TYR* 3.6 44.4 - - + +
117A PHE* 4.7 6.7 - - + -
131A TYR* 5.3 0.4 - - + -
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Residues in contact with LYS 37 (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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4A ILE* 5.3 1.2 - - - +
10A GLY 3.8 2.5 - - - +
11A ALA* 3.1 3.8 - - - +
12A GLU* 2.8 73.8 + - + +
14A VAL* 3.6 14.8 - - + +
35A PHE 3.5 2.4 + - - +
36A VAL* 1.3 70.9 - - - +
38A ASP* 1.3 58.6 + - - +
218A LYS* 6.2 1.3 - - - +
276A HIS* 3.4 41.6 + - + +
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Residues in contact with ASP 38 (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 ASP 5.1 0.5 - - - +
10A GLY 3.6 4.4 - - - +
11A ALA* 3.8 14.4 - - + +
36A VAL* 3.8 7.5 + - + +
37A LYS* 1.3 73.8 - - - +
39A LYS* 1.3 59.0 + - - +
40A LYS* 3.0 14.4 + - - +
41A TYR* 3.0 39.1 + - + +
43A LYS 5.9 0.2 + - - -
111A TYR* 2.6 31.7 + - + +
113A ILE* 3.3 20.0 - - - +
114A GLY 2.7 21.7 + - - -
218A LYS* 5.0 6.9 + - - +
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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