Contacts of the strand formed by residues 39 - 45 (chain U) in PDB entry 1IR1
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 39 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33U LEU* 4.2 1.3 - - - -
37U LYS 5.1 2.9 - - - +
38U TRP* 1.3 73.0 - - - +
40U PRO* 1.3 77.6 - - + +
73U PRO* 3.8 22.4 - - + -
74U MET 4.1 10.8 - - - +
75U PHE* 4.1 25.1 - - + -
76U GLY 5.4 1.6 - - - +
103U GLY* 3.4 1.0 - - - -
104U PHE* 2.8 52.2 + - + +
106U SER* 5.3 11.4 - - - +
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Residues in contact with PRO 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33U LEU* 4.1 19.1 - - + -
34U LEU* 4.0 13.7 - - + -
38U TRP 3.6 8.5 - - - +
39U VAL* 1.3 85.4 - - + +
41U CYS* 1.3 63.4 + - - +
73U PRO* 3.6 1.2 - - - +
74U MET* 2.8 56.8 + - + +
77U CYS* 4.2 5.6 - - + +
83U VAL* 3.9 34.8 - - + -
101U ILE* 5.2 1.6 - - + -
102U ILE 3.4 7.0 - - - +
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Residues in contact with CYS 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40U PRO* 1.3 77.0 - - - +
42U LEU* 1.3 81.0 + - - +
43U GLU* 5.0 2.0 - - - -
69U MET* 4.0 23.3 - - - -
70U TRP 4.9 0.7 - - - -
72U LEU 4.4 3.8 - - - -
73U PRO* 3.9 28.0 - - + -
74U MET* 5.3 1.1 - - - -
101U ILE* 3.7 3.5 - - - +
102U ILE* 2.9 44.2 + - + +
104U PHE* 3.8 24.0 - - + -
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Residues in contact with LEU 42 (chain U).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41U CYS* 1.3 89.3 - - - +
43U GLU* 1.3 66.7 + - - +
69U MET 3.8 0.2 - - - -
70U TRP* 2.9 46.1 + - + +
72U LEU 5.7 0.2 + - - -
74U MET* 4.6 13.5 - - - -
83U VAL* 4.6 14.4 - - + -
86U GLU* 3.8 22.0 - - + +
87U LEU* 3.5 46.2 - - + +
90U CYS* 4.5 6.1 - - + -
99U ILE* 4.5 6.1 - - + -
100U ARG 3.5 9.0 - - - +
101U ILE* 4.5 10.5 - - + -
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Residues in contact with GLU 43 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D ARG* 2.9 32.0 + - - -
41U CYS* 5.0 3.3 - - - -
42U LEU* 1.3 79.7 - - - +
44U PHE* 1.3 63.4 + - - +
66U TYR* 6.0 0.3 - - - -
67U TRP* 3.8 23.1 + - + +
68U THR 3.1 11.7 - - - +
69U MET* 4.7 7.4 - - + +
70U TRP 4.5 0.4 - - - +
99U ILE* 3.4 5.1 - - - +
100U ARG* 2.8 76.8 + - + +
102U ILE* 3.8 25.7 - - + +
111U GLN* 5.3 1.7 + - - +
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Residues in contact with PHE 44 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43U GLU* 1.3 75.7 - - - +
45U GLU* 1.3 65.3 + - - +
46U THR* 4.7 2.2 - - + -
67U TRP* 4.0 3.6 - - - -
68U THR* 2.8 60.9 + - + -
69U MET 3.7 21.1 - - - -
70U TRP* 4.1 24.5 - + + -
90U CYS* 4.2 20.9 - - - -
94U TYR* 3.6 48.9 - + - -
97U ALA* 4.3 8.3 - - + -
98U PHE 3.1 12.6 - - - +
99U ILE* 4.2 4.0 - - + -
3V VAL* 4.2 8.5 - - + -
6V THR* 4.0 14.4 - - + -
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Residues in contact with GLU 45 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D LYS* 2.9 31.0 + - - -
44U PHE* 1.3 78.2 - - - +
46U THR* 1.3 62.4 + - - +
47U ASP* 2.3 34.3 + - - +
48U HIS* 3.1 37.2 + - - +
49U GLY* 4.2 2.9 - - - +
64U GLY* 6.6 0.2 - - - -
67U TRP* 3.4 39.6 - - + +
68U THR* 4.5 3.2 + - - -
97U ALA* 3.2 4.3 - - - +
98U PHE* 3.0 35.4 + - + -
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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