Contacts of the strand formed by residues 26 - 32 (chain A) in PDB entry 3G65
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 26 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLY 3.5 0.2 - - - -
25A ASP* 1.3 88.2 - - + +
27A LEU* 1.3 59.5 + - - +
28A TYR* 3.3 33.3 + - + -
40A THR* 3.3 16.3 + - - -
41A VAL 4.7 0.8 + - - -
74A LYS* 3.2 38.2 + - + +
75A ILE 3.4 11.9 - - - +
76A LEU* 4.4 12.8 - - + +
77A MET* 3.5 4.4 - - - +
127A GLN* 4.9 5.5 + - - -
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Residues in contact with LEU 27 (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 VAL* 4.9 1.8 - - + -
20A LEU* 3.8 24.7 - - + -
26A GLU* 1.3 70.1 - - - +
28A TYR* 1.3 69.8 + - - +
29A LEU* 3.4 21.9 - - + +
38A LEU* 4.0 15.3 - - + -
39A ARG 3.6 11.4 - - - +
74A LYS* 3.4 4.2 - - - -
75A ILE* 2.8 38.0 + - + +
77A MET* 3.6 28.6 - - + +
80A PHE* 3.3 46.9 - - + -
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Residues in contact with TYR 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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26A GLU* 3.3 32.1 + - + -
27A LEU* 1.3 75.3 - - - +
29A LEU* 1.3 62.4 + - - +
37A SER 3.4 4.0 - - - +
38A LEU* 3.5 3.5 - - - -
39A ARG* 2.9 46.4 + - + +
40A THR* 4.1 3.4 - - - -
41A VAL* 4.7 8.8 - - + +
73A CYS 3.6 4.3 - - - +
74A LYS* 3.3 34.0 - - + +
129A CYS* 4.1 18.2 - - - -
130A GLU 4.3 7.2 - - - -
131A SER* 5.7 0.2 - - - -
132A LEU* 3.3 52.8 - - + +
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Residues in contact with LEU 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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1A MET* 4.9 15.0 - - + -
27A LEU* 3.4 37.7 - - + +
28A TYR* 1.3 77.3 - - - +
30A GLU* 1.3 66.3 + - - +
31A PRO* 4.3 0.9 - - + -
36A LEU* 5.1 9.4 - - + -
37A SER 3.6 3.6 - - - -
38A LEU* 5.2 7.4 - - + -
72A ARG* 3.3 4.1 - - - +
73A CYS* 3.0 51.9 + - - +
75A ILE* 4.4 12.8 - - + -
80A PHE* 5.0 7.9 - - + -
99A ILE* 5.5 2.7 - - + -
108A LEU* 3.6 31.9 - - + -
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Residues in contact with GLU 30 (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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29A LEU* 1.3 78.7 - - - +
31A PRO* 1.3 68.9 - - + +
32A LEU* 3.5 28.5 + - + +
36A LEU* 4.1 2.5 - - - +
37A SER* 3.1 41.1 + - - +
39A ARG* 3.3 27.4 + - - +
72A ARG* 4.3 12.8 + - + +
131A SER* 2.9 40.3 + - - +
132A LEU 4.5 0.2 + - - -
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Residues in contact with PRO 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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1A MET* 3.3 41.7 - - + -
29A LEU* 4.3 0.7 - - + -
30A GLU* 1.3 88.6 - - + +
32A LEU* 1.3 69.8 + - - +
35A GLY 4.0 4.9 - - - +
36A LEU* 4.1 4.0 - - + -
59A GLN* 4.0 14.8 - - - +
61A TYR* 4.2 24.1 - - + -
71A LEU* 4.0 30.5 - - + +
72A ARG 4.3 0.7 - - - +
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Residues in contact with LEU 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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30A GLU* 3.5 28.3 - - + +
31A PRO* 1.3 82.9 - - - +
33A GLU* 1.3 60.8 + - - +
34A ASP* 3.0 28.6 + - - +
35A GLY 2.8 18.1 + - - +
37A SER* 4.2 20.0 - - - -
39A ARG* 4.3 13.7 - - - +
52A LEU* 4.4 6.5 - - + -
59A GLN* 3.7 10.9 + - - +
61A TYR* 4.7 10.8 - - - -
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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