Contacts of the strand formed by residues 39 - 45 (chain V) 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 V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37V LYS 4.9 4.0 - - - +
38V TRP* 1.3 74.8 - - - +
40V PRO* 1.3 70.5 - - - +
73V PRO* 3.9 8.7 - - + -
74V MET 3.8 29.2 - - - +
75V PHE* 3.9 29.8 - - + +
76V GLY 5.5 1.8 - - - +
102V ILE 3.7 0.2 - - - +
103V GLY* 3.3 3.6 - - - -
104V PHE* 2.8 51.7 + - + +
106V SER* 5.5 10.3 - - - +
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Residues in contact with PRO 40 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V VAL* 6.0 0.7 - - + -
33V LEU* 3.8 19.9 - - + -
34V LEU* 4.0 13.2 - - + -
38V TRP 3.5 9.4 - - - +
39V VAL* 1.3 86.3 - - + +
41V CYS* 1.3 63.3 + - - +
73V PRO* 3.6 0.9 - - - +
74V MET* 2.9 52.9 + - + +
77V CYS* 4.2 4.3 - - + +
83V VAL* 3.9 35.0 - - + -
101V ILE* 5.2 1.6 - - + -
102V ILE 3.4 7.0 - - - +
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Residues in contact with CYS 41 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ARG* 6.3 0.2 - - - -
40V PRO* 1.3 76.0 - - - +
42V LEU* 1.3 79.5 + - - +
43V GLU* 5.0 1.8 - - - -
69V MET* 3.9 22.7 - - - -
70V TRP 4.9 1.1 - - - -
72V LEU 4.4 3.4 - - - -
73V PRO* 3.8 29.2 - - + -
74V MET* 5.0 2.2 - - - +
101V ILE* 3.7 3.3 - - - +
102V ILE* 2.9 44.2 + - + +
104V PHE* 3.7 24.5 - - + -
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Residues in contact with LEU 42 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41V CYS* 1.3 89.9 - - - +
43V GLU* 1.3 64.2 + - - +
69V MET* 3.8 1.7 - - - -
70V TRP* 2.9 47.6 + - + +
74V MET* 5.0 6.3 - - - -
83V VAL* 4.3 26.2 - - + +
86V GLU* 3.8 16.6 - - + +
87V LEU* 3.6 41.7 - - + +
90V CYS* 4.4 7.4 - - + -
99V ILE* 4.5 6.7 - - + -
100V ARG 3.5 8.7 - - - +
101V ILE* 4.3 14.1 - - + -
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Residues in contact with GLU 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ARG* 3.0 30.8 + - - -
41V CYS* 5.0 3.0 - - - -
42V LEU* 1.3 80.1 - - - +
44V PHE* 1.3 62.2 + - - +
66V TYR* 6.1 0.5 - - - -
67V TRP* 3.9 22.8 + - + +
68V THR 3.1 11.7 - - - +
69V MET* 4.8 7.5 - - - +
70V TRP* 4.5 0.4 - - - +
99V ILE* 3.4 6.4 - - - +
100V ARG* 2.8 76.1 + - + +
102V ILE* 3.7 28.0 - - + +
111V GLN* 5.1 1.2 + - - -
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Residues in contact with PHE 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3S VAL* 4.1 12.1 - - + -
6S THR* 4.0 17.5 - - + -
43V GLU* 1.3 76.4 - - - +
45V GLU* 1.3 64.1 + - - +
46V THR* 4.8 2.2 - - + -
67V TRP* 4.0 2.9 - - - -
68V THR* 2.8 64.6 + - + -
69V MET 3.8 17.0 - - - -
70V TRP* 4.1 20.6 - + + -
90V CYS* 4.2 19.7 - - - -
94V TYR* 3.5 50.5 - + - -
97V ALA* 4.3 7.4 - - + -
98V PHE 3.2 12.3 - - - +
99V ILE* 4.3 4.7 - - + -
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Residues in contact with GLU 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A LYS* 3.0 31.3 + - - -
44V PHE* 1.3 78.0 - - - +
46V THR* 1.3 64.3 + - - +
47V ASP* 3.0 26.0 + - - +
48V HIS* 3.1 41.9 + - - +
49V GLY* 4.3 1.8 - - - +
67V TRP* 3.5 36.8 - - + +
68V THR* 4.5 3.6 + - - -
97V ALA* 3.2 1.6 - - - +
98V PHE* 2.9 34.7 + - + -
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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