Contacts of the strand formed by residues 34 - 39 (chain P) in PDB entry 1IBM
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 GLU 34 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20P VAL* 3.3 4.3 - - - +
21P VAL* 2.8 27.9 + - + +
32P TYR* 3.4 10.2 - - - -
33P ILE* 1.3 90.7 - - + +
35P LYS* 1.3 69.1 + - - +
36P ILE* 3.2 15.2 - - - +
55P ARG* 2.8 51.2 + - - +
59P TRP* 3.4 17.6 + - - +
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Residues in contact with LYS 35 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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626A U 2.7 30.1 + - - -
627A G 4.1 16.3 + - - -
18P ARG* 2.9 42.1 - - + +
19P ILE 3.8 5.2 - - - +
20P VAL* 4.3 1.1 - - + +
32P TYR* 3.7 22.6 - - + +
34P GLU* 1.3 86.2 - - - +
36P ILE* 1.3 70.1 + - - +
37P GLY* 3.5 25.1 - - - +
38P TYR* 4.4 8.0 - - - +
50P LYS* 5.8 3.8 - - - +
55P ARG* 5.6 0.2 - - - +
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Residues in contact with ILE 36 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P ILE* 3.7 30.5 - - + -
19P ILE* 2.8 26.4 + - + +
20P VAL* 4.5 2.2 - - - +
21P VAL* 4.3 19.1 - - + -
34P GLU* 3.2 29.4 - - - +
35P LYS* 1.3 73.4 - - - +
37P GLY* 1.3 58.0 + - - +
50P LYS* 3.7 8.1 + - - +
51P VAL 2.5 35.5 - - - +
52P ASP* 3.4 8.1 - - - +
55P ARG* 3.7 19.5 - - + -
56P ALA* 4.1 25.4 - - + +
59P TRP* 4.3 2.9 - - + -
74P LEU* 4.7 3.4 - - + -
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Residues in contact with GLY 37 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P ARG 3.5 0.7 - - - -
19P ILE* 2.7 38.5 + - - +
35P LYS* 3.5 17.3 - - - +
36P ILE* 1.3 83.2 - - - +
38P TYR* 1.3 61.2 + - - +
50P LYS* 3.6 22.2 - - - -
51P VAL* 4.4 0.7 - - - -
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Residues in contact with TYR 38 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625A G 5.0 4.3 - - - +
626A U 3.6 64.1 + - - +
627A G 4.5 1.6 - - - -
16P HIS* 6.4 2.0 - + - -
17P TYR 3.6 13.0 - - - +
19P ILE* 3.9 4.1 - - - +
35P LYS* 4.4 8.7 - - - -
37P GLY* 1.3 77.7 - - - +
39P TYR* 1.3 69.8 + - - +
40P ASP* 5.1 1.6 - - + -
47P ASP* 2.9 47.3 + - - +
48P TRP* 4.9 1.6 - - - -
49P LEU* 3.5 12.5 - - - +
50P LYS* 3.4 59.5 + - + +
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Residues in contact with TYR 39 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375A U 6.4 0.7 - - - -
451A A 4.9 7.8 - - - -
452A A 4.3 6.2 + - - -
6P LEU* 4.2 8.5 - - + -
16P HIS* 3.8 2.6 - - - -
17P TYR* 2.9 53.4 + + + +
19P ILE* 4.3 6.1 - - + -
38P TYR* 1.3 83.9 - - - +
40P ASP* 1.3 71.2 + - - +
41P PRO* 3.1 41.7 + - + +
43P LYS* 5.2 0.5 - - - -
48P TRP* 3.7 26.4 - + - -
49P LEU* 3.9 5.8 - - + -
69P THR* 5.5 3.4 - - + -
72P ARG* 4.0 17.2 + - - -
73P LEU* 3.4 49.4 - - + -
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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