Contacts of the strand formed by residues 39 - 44 (chain A) in PDB entry 4IRX
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 39 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A PRO 4.4 1.4 - - - +
34A ARG* 3.5 43.7 + - + +
35A GLY* 2.9 25.1 + - - -
36A SER* 3.6 15.4 + - - +
37A HIS 2.9 5.3 + - - +
38A MSE 1.3 79.5 - - - +
40A VAL* 1.3 70.0 + - - +
41A VAL* 6.6 0.2 - - + -
68A VAL* 3.6 1.2 - - - +
69A LYS* 3.1 36.0 + - + +
71A GLN* 3.3 29.1 + - + +
94A ALA* 5.8 0.2 - - - -
95A LYS 5.3 0.2 + - - -
96A VAL 4.7 4.5 + - - +
295A ILE* 3.7 9.0 - - - +
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Residues in contact with VAL 40 (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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39A GLU* 1.3 80.6 - - - +
41A VAL* 1.3 79.0 + - - +
42A VAL* 4.1 4.3 - - + -
68A VAL* 3.9 11.2 - - + -
69A LYS 2.9 6.5 + - - -
70A VAL* 3.2 9.3 - - + +
71A GLN* 2.9 24.5 + - - +
94A ALA* 6.3 0.4 - - - -
96A VAL* 3.8 15.0 - - + +
98A ILE* 3.9 28.7 - - + -
288A LEU* 4.1 11.7 - - + -
291A ALA* 3.9 18.6 - - + -
292A VAL* 5.2 0.9 - - + -
295A ILE* 3.7 20.0 - - + -
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Residues in contact with VAL 41 (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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31A LEU* 3.9 15.7 - - + -
34A ARG* 6.2 0.4 - - - +
40A VAL* 1.3 78.8 - - - +
42A VAL* 1.3 64.2 + - - +
43A SER* 4.1 2.0 - - - +
71A GLN* 3.5 14.4 - - + +
73A LEU* 3.7 29.6 - - + -
86A LEU* 5.1 1.1 - - + -
89A ALA* 3.9 24.2 - - + -
94A ALA* 4.0 13.9 - - + +
96A VAL 3.5 5.1 + - - -
97A VAL* 3.3 24.3 - - + +
98A ILE 2.9 25.1 + - - -
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Residues in contact with VAL 42 (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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40A VAL* 4.1 15.0 - - + -
41A VAL* 1.3 79.0 - - - +
43A SER* 1.3 62.5 + - - +
44A PHE* 3.6 30.4 + - + -
59A LEU* 3.9 33.2 - - + -
70A VAL* 4.2 12.3 - - + -
71A GLN 2.9 10.2 + - - +
72A VAL* 3.3 6.3 - - + +
73A LEU 2.9 26.8 + - - +
98A ILE* 3.3 25.1 - - + +
124A VAL* 5.8 1.1 - - + -
284A ILE* 4.6 5.2 - - + -
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Residues in contact with SER 43 (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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41A VAL* 4.1 0.6 - - - -
42A VAL* 1.3 71.9 - - - +
44A PHE* 1.3 63.2 + - - +
73A LEU* 3.6 18.4 + - - +
75A ALA* 4.9 1.2 + - - +
82A GLN* 3.0 32.6 + - - +
85A ASP* 5.1 2.3 + - - +
86A LEU* 3.8 26.3 - - - +
97A VAL* 4.9 0.9 - - - -
98A ILE 2.9 11.8 + - - +
99A VAL* 3.6 4.3 - - - -
100A ALA* 2.9 26.5 + - - +
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Residues in contact with PHE 44 (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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42A VAL* 3.6 28.7 - - + -
43A SER* 1.3 73.8 + - - +
45A ASN* 1.3 60.6 + - - +
46A ASP 4.4 3.4 - - - +
47A LEU* 3.7 23.3 - - + -
52A PHE* 3.8 43.1 - + + -
55A MSE 4.1 18.6 - - + -
56A ARG* 4.1 25.1 - - + -
59A LEU* 4.0 10.8 - - + -
72A VAL* 3.7 29.8 - - + -
73A LEU 2.8 10.7 + - - +
74A ASP* 4.8 0.7 - - - -
75A ALA* 2.9 29.3 + - - +
82A GLN* 3.9 1.3 - - - -
100A ALA* 3.9 7.2 - - + -
124A VAL* 5.7 2.0 - - + -
284A ILE* 4.9 3.8 - - + -
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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